Added PTL2 Scripts

These are PTL2 files from Auden 2/9
2025-12-27 04:00:25 +08:00 · 2023-02-14 11:20:52 -05:00 · 2023-02-14 11:20:52 -05:00 · dd76ab1d12
commit dd76ab1d12
parent 18e07170be
2151 changed files with 2517388 additions and 0 deletions
--- a/.DS_Store
+++ b/.DS_Store
--- a/PTL2/Data/.DS_Store
+++ b/PTL2/Data/.DS_Store
--- a/PTL2/Data/Pre-Guidance/OG5_126946_preguidance.faa
+++ b/PTL2/Data/Pre-Guidance/OG5_126946_preguidance.faa
@ -0,0 +1,53 @@
+>Sr_st_Pinf_XX_002901480_Contig_6403_Len1230_OG5_126946
+MKMPSALSFEVLGRHHRARAATLTLPHGEVRTPVYMAVGTQGAIKGLTTQQMQEQPVDCQIFLANTYHLALRPGTEVLAQLPGKLHEFMQWPRNLLTDSGGFQMVSLSRLCQVSEHGVQFESFVDGSTMLLTPEASIAHQNRIGADIIMALDDVVSSLTDDDERFKEACGRTVRWLDRCIQAHAHPDKQNLFGIVQGGLDVSEGGLRDQCLTELIKRDLPGYAIGGLAGGESKEAFWKVVAKCTAQLPENKPRYLMGVGYPLDLVVCSALGVDMFDCVYPTRTARFGTAIVPSGLLKLKSAKCELDSRPIDDTCECFVCKKYTRAYLRVLLKKEETFGDAEATTGSIGAHLVTYHNVTYMLNLMRRLRQSIIDRKFEQFVQNFMLQQFPERNYPQWAVDALTEAKISLN
+
+>Am_tu_Hpap_XX_Contig_6294_Len585_Cov1_OG5_126946
+CLAEFQKRDLPGYAIGGLSGGESKDEFWKIVSQCTSKLPSNKPRYLMGVGFPVDLVVCVALGVDMFDCVYPTRTARFGTALVPTGAINLKLTIYANDFRPVDETCSCLTCHGYTRAFLHSKSRGDSIGAVLLSYHNIAYQLRLMGELRQSIIEGQFSKYVQQFMLKQFPKMDYPKWVVDSLGSVGISLHTTVSQ
+
+>Sr_ci_Ptet_XX_001454454_Contig_8002_Len1797_OG5_126946
+MYNGMNMYHTLENWQSIKCTIQVQQRTVSVMLQNLPFKDPNKKGNPNLESLKVKFILIPDTYIEGVVGQRIQLKVYEADLCIRFPNVRYLSKGDPYVTFFLTEDMERNYNWKIKKRLSNIQLVNDKFDLENKSYCQKLQFNKLDLFKNQVSRLTLFIIFYTSVYFPIFSTQNIFFSNIFNLIYHLIQQIMQELGDIENQPHKKVKTNETPLEFTVLATHNFARASIMRLPHGEVLTPVYMPVGTKGAMKGVTYSEMDDLGCKLLLANTYHLAYKPGGNLLEKVGGLHNFVNWKHNILTDSGGFQMVSLSQLSEVTEEGVTFESPYDKSTMHLRPEDSIHTQNQIGADIIMALDDVVRTTTVGPRMQEASERTTRWLDRDIAAHKRKHDQNLFPIVQGGIDPKLREQSLNDLIQREANGYAIGGLAGGEDKVDFWKTVAQCTATLPVNKPRYLMGVGYPVDVVVCSCLGVDMFDCVFSTRTARFGTAFTDNGFLKLKNKEAANVFEPIQKGCQCQACKSYTQSYIHYLIAREEVACHLISVHNLNYLIQLMLNLRQSIIDGKLIEFINEFLKKWFKNEGQIPVWIIEALEYAKIPVEQL
+
+>Sr_st_Bhom_XX_012897755_Contig_1728_Len1251_OG5_126946
+MKYDTPALVFDIVKKWNRARASVMTLRHGPVLTPVFMPVGTKGTIKGLTPDQMRDEPMDCQILLGNTYHLSSKPGAQEVADFGGLHKFMQWDRNILTDSGGFQMVSLLDLAEITENGVVFRHPADGSRLVLRPEDSIHYQNLIGADIIMALDDVVHSCTNDDARFTEATHRTVRWLDRCIAAHSRKDEQNLFAIVQGGLDVSDNGLRNQCLDAFLERADSIPGFAIGGLAGGEDKESFWRVVELCTRRLPADKPRYVMGVGYPLDIVVCTALGADMYDCVYPSRTGRFGTAMVPWGLLKLKSKACAEDLRPIDPDCTCRTCKNYSRAALHQLCKKEALGASLVTEHNLHYMIHFMREMRMSIIEGRFDAFVREFMRKYFPKGDVPKWCVDALRVAGIDLVESSSVCVQTEEIMDWM
+
+>Ba_ba_Bcae_XX_065538610_Contig_1463_Len1131_OG5_126946
+MTFELQYTDTKSNARAGLITTDHGQIQTPIFMPVGTLGTVKGVHLTELKEDIQAQIILGNTYHLYLRPGLDVIEKAGGLHRFNGFDRPMLTDSGGFQVFSLAGIRKLREEGAEFRSHIDGNKHIFTPEKVIDIERTIGADIMMAFDECPPGDSDYEYAKKSLGLTHRWLDRCIQRFNETEPKYGYKQALFPIVQGCVYPDLRKQSAEFIASKGAEGNAIGGLAVGEPVDKMYEMIEIVNEILPKDKPRYLMGVGTPVNILEGIERGVDMFDCVMPTRNGRNGMLFTKDGIINMRNKKWETDFSPIEADGASSVDTLYSKAYLRHLFHAQELLAMQIASIHNLAFYLWLAGEARKHIIAGDFSTWKPMMVKRVSTRL
+
+>Am_tu_He47_XX_Am_tu_He47-LKH612_4233_Len1044_Cov6_OG5_126946
+DQLSSLGPPIILGNTYHLGHRPGPEVLSKMGGLHTFMGWNKNILTDSGGFQMVSLLKLADITEEGVKFESPHDGSELLLTPEKSIQIQNEIGADIIMALDDVVSSTITGPRVEEAMHRTIRWIDRCIAAHRRPHDQNLFGIIQGGLSSHLRDICLAEFKKRDLPGYAIGGLSGGESKDEFWKIVSQCTSNLPSNRPRYLMGVGFPVDLVVCVALGVDMFDCVYPTRTARFGTALVPTGTLNLKLTIYANDFRPVDETCSCLTCRSYTRAFIHCKSRGDTIGAVLLSYHNIAYQLRLMGELRQSIIEGQFSKYVQQFMIKQFPKMDYPKWTLDALDSVGISLLTTMTE
+
+>Sr_rh_Blon_XX_Contig_15473_Len669_Cov5_OG5_126946
+RTLRWIDRCIKAHKNKHRQNLYGIVQGGLDAKLRDYSLKEMIKRDLPGYAIGGLAGGEDKALFWRVVKQCCDVLPKDKPRYLMGVGYTLDLVVCSALGCDQFDCVYPARTARFGTAMTSEGLIPLKKRKYSCDNRILDPTTSVGRNYTRGFLHEALKESTGCQLLTMHNIEFLQNFMKRLRASIRDGTFPDFVRDFMKREHPDGKYPQWAVNALRAAGIALT
+
+>Sr_rh_Blon_XX_Contig_7214_Len969_Cov5_OG5_126946
+AGTQLMFCNTYHLIVHPGADVVEKAGGLHKFMNRSSPIITDSGGFQVFSLAEATSEDGDELKSRGNKRSTGSLLKVSEDGVLFRSYFDGSKISLTPEGSVRAQKMLGADIIVPLDELPPYHVTAKRLKESVYLSHRWEARSLKEHLKNPQQQAMYAVIHGGVDRELRKLSAEYLSSLPFDGFAVGGSLGKDRREMAELLQYVMPLLPEDRPSHVLGIADTESIESTVSFGCDTFDSAYPTRVARHGTLFTTDGLIHIKLSRFKEDYGSIDPKLETIPYSRSYLHHLLRAKEPLFLTLASLHNMIYMNKMMADIRERILRDEI
+
+>Op_me_Bplu_XX_Contig_9582_Len1137_Cov7_OG5_126946
+KCKHTKARVSVLRLPHGVVDTPVFMPVATKGTLKGLTTKQINELNCQIILGNTFHLGSKPGVNILNQKNGLHGLMNFDNNILTDSGGFQMVSLLKLSHVTEDGVTFNHPDTNEEIVLTPEHSMEIQMSLKSDIIMQLDDTVSSLTTGERVSIAMQRSIRWLDRCINVVAKSINQNLFPIVQGGLDINLRTECINEMLKRNLPGYAIGGLSGGEMKESFVKIVDHCTNMLPTSKPRYLMGVGYAPELVICTALGCDMFDCVYPTRTARFGTALINHVNNLQISHFSNKNDLNPIDSSCTCTTCKKYSRAYLHSLFVTNNPVVLSLLTVHNITYQKRLMESIKLSIIEDRFVEFIHIFFKSYFDEIPIWVDKFLTTLIDC
+
+>Za_ec_Maeo_XX_011973592_Contig_63_Len1959_OG5_126946
+MFEIKHRDAMGRIGKLKINGKIIETPTIMPVVHPNPKKQTVSIEKIEKLASVIITNSYIINTNPELKKIAEEKGIHNLIGFDKVIVTDSGSFQLSVYGEITVEPEEIIEFQEKIGVDVGTILDIPTAPYVQREQAEEELKETLRRAELSVKLRDEKNYKLLLNGTIQGSTYMDLRQESAKKMKELDFDIYPIGAVVPLMENYDYAQVIEIILNSKKELPTNKPVHLFGCGHPMMFALSVALGCDLFDSAAYALYAKDGRYLTESGTLHLEDLKDLEKFPCSCPVCIEYTPKELAKMEKRKRTELLAEHNLYITFEEINRIKQAIKDGNLWELVEERCRAHPKLLEAYRKALEYNEFIEEFDPITKKSAFFYGGYESLYRPEIIRHKKRLERIKSDNIYITTISNDINRPYSENTNMMDSDALVLIKDDLFGLVPLSIDTVYPLSQCDNPKLYCYEKIHNNEFVEEFKQNNKDKIMDITSYNYYINHYTSNANKNKVGSDAIRINNMIQYQYGFKLNDEELKKLIIKRSKKTNRIRNVLIPTDGNNKEVLFTLRSNDNLLIPAKEGAKLIHEKLPFPKYRVVIDSEVEEFARDGKSVFSKFVINCDKELRPYEEVIIVNENDELLAYGTTLLNGKELGEFNYGAAVSVRSGFK
+
+>Za_et_Tkod_XX_011249711_Contig_141_Len1743_OG5_126946
+MVDFRFEVKARDASGRIGKLTVNGKTVETPAIMPVINPKQLIVTPKELKEMGFGMIITNSYIIYKTPELREKALEVGIHKLLDYDGIIEVDSGSFQLMRYGGVEVTNREIVEFQHEIGVDIGTFLDIPTPPDAPREKAEEDLRITLERAKEAEEIKEIAMNAAVQGSTYPDLRTYAARELSRMNFEIHPIGAVVPLMESYRYRDLVDVVIASKVGLRPDRPVHLFGAGHPMIFALAVAMGIDLFDSASYALYAKDDRYMTPEGTKRLEELEYFPCSCPVCSRYTPQELREMPKEERTRLLAIHNLWVIREELNRVKQAIKEGELWRLVDERARSHPKLYAAYKRLLEYREYLEKNEPVTKASAFFKVSEEALRWPIVERARERAERVRSKFPETISHPIFGEIPKYLSLSYPFAQSEGEEDFTVEKPEKGEARKYVMAVAEYQFGEGAGEAFKDAFVELSRKTGMPRQIKAKGKHLATFRAEDGLLTLGIEGAKRLHEVLPFPRMRVVVDEDAEPFARRGKNVFAKFVVDADLNIRPYDEVLVVNRNDELLATGQTLLNGEELKIFQQGLAVKVRRGVEK
+
+>Za_as_Loki_XX_KKK40305_Contig_418_Len1653_OG5_126946
+MRWEILDTDALGRIGKLEIKGKKMDTPNLFPVLHPYKNIISSSEFKKIGAQCVFTNSYIIHQNANVKEQVLKRGLHKYLEFDGIIATDSGAFQQYMYNNTDFEINAEEIERFQELIRSDFPVILDLPVQPNDDYDTVKKKIITTIDRAKNNIDRRTNPDCIWFGPIHGAKYLDLLEFSTVEMSKLDFGILALGGLVKYFLNYRYDLVLKALLTVKKASISNRPLHLFGLGLPQFFSLAILCGCDLMDSAAYVLYAKENRYFTLSTGTKQLDELDEFPCTCPICLEYTPKELRSLDKVKQTELLAKHNLYISFAELRTIRQAIKEGNLWELVEQRIRSHPTLVNALKSIKDNVALFEIHEKIYKPHGRLFVSSDSVNRPLIYRYVLKLNQYYRPPRCGKFLIILPELDVKGEYSPSIKNWLENINENSIIPRKLLHVVFLSDFFGIIPLELSYTFPMGQSELIVLQEKENVAFQSTVKKVGTYLNTNLKHYDMCGLFIPDKIINQFNEITEFTKTGLMEKITPLLKSKFNSKFTISNEITQLLQFFKESLQ
+
+>Ba_cd_Cavi_XX_020356259_Contig_285_Len1119_OG5_126946
+VALKFHVLHQSKKSQARVCQIETAHGTIDTPAFVPVATNGALKGVLDHSRIPLMFCNTYHLLVHPGTQHIAAMGGLHKFINRHAPIITDSGGFQIFSLAYGSVTEEIKSKGKKKHSSSILNITDDGVWFKSYRDGSKLFLSPETSVQAQKDLGADIIIPLDELLPFHTDTNYFLSSCSRTYIWEKRSLDYHRQSPGYQSMYGVIHGGIDPKQRKIGCQFVEEHPFDGFAIGGSLGRNFQEMVNVVDITMRYLSKDRPVHLLGIGDLPSIRAAVKFGIDSFDSSYPTKIARHGLILSSPKPIKIDNHAYSQDPTPIDPNCHCLTCTSNISKAYLHHLFKVHEPNAGIWASIHNLHYMQEVMKTIREQILNDEI
+
+>Ba_cy_Smaj_XX_072620615_Contig_1298_Len1152_OG5_126946
+MSSPVASAFQFHIDATCSQTQARAATFQTPHGIVETPRFMPVGTVGTIKGLTPAQVEATQAQMILANTYHLHLQPGEALVQAAGGLHQFMGWQQPILTDSGGFQVFSLSKLRKLTEDGVTFQSPRDGRKIHFTPEKSIQIQNALGADVIMAFDECPPYPATREAVEAATQRTFRWLERSIAAHERPQDQALFGIVQGGIYPDLRIEAAQQLVALDLPGYAIGGVSVGEPPELMYPVVEATTPILPAHKPRYLMGMGTYREMVRAIAAGIDLFDCVIPTRFGRHGTAMVQGERLNLKNAQFREDFTPLDPTCPCYCCTTFSRAYLNHLVKAKEMLAYILLSLHNVTELVRFTQQIRASILSDRFVEDFGPWLTDPDPKDCGQAD
+
+>Am_ar_Mabd_XX_Contig_8695_Len1002_Cov4_OG5_126946
+DQLKRLGGLHKFMRWPNAILTDSGGFQMVSLCKLSNVTEEGVTFQSPRDGNMSLLTPERSMEIQMAIGSDIIMALDDVVRPTDDAKRIAEASERTVRWLDRCCATLPNRGHGPTQSLFAIVQGGLDGGLRDRCLDELIKRDTPGYAIGGLAGGESKDSFWRVIAFCCERLPQNKPRYAMGIGYAEDMLVCVALGVDMFDCVYPTRTGRFGVALTDAGPLNLNQSSNSQCVDVITPGCPCNACSQGYSKACLRAMFCGPTGTEVAAQLVTHHNIAFQLGLMRRAKAAIENNTFPEFVSRWMINRYGGQLSSVPQWIHEALTHAGISMAQFVKQQ
+
+>Sr_di_Smic_XX_OLQ08674_Contig_5990_Len4278_OG5_126946
+MSIREENVKREDSDIADFMALAQSFRFRRFALSFSFSGKDIGCLELGSVSPRLPVPSEVSEQAEGRAPALPGEGASEAPASSDWRMVLYHDRNVVLFNPGEKPAFRSRRLSVDEAAPGTELSNPSGRCPLCRQTVDARFAFAAQAYFDLLQGLFRSGTRDPEGEDIDLLAESDLYRILGLPRSAKADDIKRAYRKRSLRFHPDKNPDDPDAKLKFQKVAEAFTVLSDENKRAKYDNSGDMDLEGFDVETFMEMVNAAGLKFQKQDRGSDERDGRDDFPEEVPSRSAMDRLAGLGVSDEEQGDAIAIGDGDYDANPFLLGAEASNPAEVPIFASEGGAEAQQAAAAALRHLPAGLLNTGYYVRFFQETKLLGSGSFGAVYLCRHVLDDMMLGDYAVKKVPVGDNKVWLRDMVREDAMSKRKLEDAQAEANRPSQAGRPPLVFHLEATCGRARAATVTLPHGDVLTPVFMPVGTQGTIKGMSSEDMEMLGCRILLGNTFHLANRPTCELLRKCGGLHKLMNWNGNILTDSGGFQMVSLLKLAVITEDGVEFEDPKKPGSRMLLTPEKSIESQNDIGADIMMALDDVVSSTLDPVKDEARIKEATDRTLRWIDRCMKAHRNPEQQNLFGIVQGHLDVKDGGLRDYSLKEMIKRDLPGYAIGGLSGGEAKSEFWRVVERCTRPESGLPPMKPRYLMGVGYPLDIVICVALGVDMFDCVYPCRTARFGTALVRSGQLRLTSAEFASDYRPLEPDRDGNGQGPLKDYTRAMLYTIVTKEPVAAQLITLHNLWFMLNLLQEMRQQIKSGSFPEWVRRFLQDFFPIAKPAPCEHCPPRWVKDALDLCGIAVDDLFDWSESAKELPDMPKDTGKASGLQRVALISLTGENVKTFERLHHPNIVEYKHSWLELSRRSEFCPFVPFLFILMQYCNGGSLAEQIWHDGNSQTPKDQMPTEQIWHFLLDILLGLQHLHRQGILHRDLKPTNILLSWPDNSNRGAGSEMFPRALLSDFGTAQAFGEPPASATAAASRGYTGTVEYTAPELLLMEDFEREYSEKSDMWSLGMVLYAMCFSSLPFSHDDPHVVKGLIKSFVEEKRRAAPNEKAPSAEEDASGWLPFDTGGRIGPLRLVLAALLALDARRRPAATDLLENTVFRRQARRYLRKADPAGEAQTTALPIDSSWNWLPFGLKYNMLWRKALVGCMEAVGFFARHAIRHSEKSEVPERLSSGLHKAMKAMASMKGQAVPMNVMKSMKKGLTAGTWAAAKKKAEQEEQDPVEALKLAKRIYGRQVFLERRPPAAAAAPPSFGILADLSLASIAFDAGLGTLERNAEGRYRLANGATKVNVRLPQCIEEVLGPVKDYNPKQVEEWCNSLGQVVLEKMQELSGNFKHRAQAGLRYIVNISLMEKKGAGFHTRWENKALICVVQVFGIGM
+
+>Za_eh_Hvol_XX_004041882_Contig_388_Len1551_OG5_126946
+MRDHFELRDGDLAGRIGRLSVPRAGVTVETPALLPVVNPNIDTISPARLESEFGAEILITNSYIIKTNDHLREEALDVGLHEMLDFDGAIMTDSGSFQLAEYGEIDTTTEEILQFQRDIGTDIATPVDIPTPPDVAREQAEADLEITRQALADAEAADTGEMLVNAPVQGSTYPDLREEAGRHADATDLDVFPVGAVVPMMNAYRYDDMVDAVAAAKRGLGVDAPVHLFGAGHPMMLALAVALGCDLFDSAAYALYARDGRYLTVRGTEHLEDLDYLPCTCPICTEYSPDDLREKGSKRQEQLLAEHNLHVTFAELRRIKQAIRDGDLMELVEERARSHPAMLDGYRALLAHVDQLEREDPASKGAFFYASNESAHRPEVARHHARMDRLTAEGHVLLTEGGVPSGDDFDATWRVVPPFGPFPRSLSETYPLTAEVPERLDRDAYEQAARGVSRLVEENPDAAFTLAHDDWPESALARVPESVELESLSAVSERLGDEASVGGDDGDDGGSASSAE
+
+>Ex_eu_Egym_XX_Contig_4307_Len1101_Cov5_OG5_126946
+MPVGTQGTIKGLTSEQLEGLDLDIILANTYHLGLRPGEDVLTAMGGLHSLMSWPRNILTDSGGFQMVSLLELANITEEGVEFQSAHDGSRINITPEKSIEVQNCIGSDIMMQLDDVVHVSTTGPRVEDAMWRSIRWLDRCIVANQHPKQQLFAIIQGGLDFDLRTKCIDEMVKRDNPGYAIGGLSGGESKDEFWRIVVHCTERLPANKPRYCMGVGYPVDLVVCSALGVDMFDCVYPCRTARFGSALTSCGKINLTQNKFKMDFGPLDPNCNCMTCKHYTRAMLHSICAKEQLVANLLTYHNLYYLKKLMWSLRQSIIEGAFPSFVRNFMKQQFPDLIYPRWVVEALQYVGIALDSPSHSEDVAST
--- a/PTL2/Data/Pre-Guidance/OG5_126966_preguidance.faa
+++ b/PTL2/Data/Pre-Guidance/OG5_126966_preguidance.faa
@ -0,0 +1,59 @@
+>Ba_ac_Srap_XX_020868589_Contig_2869_Len1179_OG5_126966
+VSLPPLVEPAPELTVDEVRRYSRHLIIPDVGMDGQKRLKNAKVLCVGAGGLGSPALMYLAAAGVGTLGIVEFDEVDESNLQRQVIHSQADIGRSKAESARDTVLGINPYVNVVLHEGRLEADNVMEIFSEYDLIVDGTDNFATRYLVNDACVLLNKPYVWGSIYRFDGQASVFWSEHGPCYRCLYPEPPPPGMVPSCAEGGVLGVLCASIGSIQVTEAIKVLTGTGDPLVGRLMIYDALEMTYRQVKVRKDPDCAVCGPNPTVTELIDYEAFCGVVSDEAQEAAAGSTITPKQLKEWIDDGENIDIIDVREPNEYEIVSIPGARLIPKDGFLMGGALQDLPQDKKIVLHCKTGVRSAEVLAVLKSAGFSDAVHVGGGVIGWVNQIEPDKPVY
+
+>Sr_st_Pinf_XX_002909030_Contig_9044_Len921_OG5_126966
+MTCSRCLDLEHKLAELRAQNAQLQYQLEAFQSPEKVPAEDQQGDNGEELSDTLTYSPFSRVELQRYGRQMLVKAFGFKAQLTLRSARVLMIGVGGLGSPASMYLAAMGVGTLAIVDDDTVDRSNLHRQILHDEQGARKREKKVESAKRRLQELNPLLKCVVYPTGFTPTNAFKLVGDYDVVVDASDNVGTRYLANDVCARLHKPLVSGSALGLEGQVTVFTYKDDANATGCYRCLYPTPPRVAMSCAENGVVGVVPGVIGCLQAMETVKIITGIGEPLVGVQCFYDAGIQIVRPVEDKLLSLKSKT
+
+>Am_tu_Hpap_XX_Contig_7555_Len420_Cov1_OG5_126966
+LKGFSLMGLGAQGGVLYVTDMDTIEVSNLSRQFLFRRDNVGQQKSVCASKAALQMNPEMNIKCFEVPVGPDTETKFNDGFWSKLDGVCNALDNIKAREYTDSKCVFYGKPLLESGTLGTKANSEMVIPHKTKSYAEHEIG
+
+>Am_tu_Hpap_XX_Contig_3139_Len813_Cov1_OG5_126966
+IVDNDTVELNNLHRQIIHTEAREGTSKAYSAGETIQRFNSNTDCVVYNVRLNSTNALEIIKHYDVVLDCSDNVPTRYLVNDACVLLKKPLVSGSAMGMDGQVTVYNFGSGPCYRCIYPKPPQPETVGNCANNGVLGVVPGIIGSIQALECIKIIVGCGSVISQKLVLFNALKMQFHTIMLPEKKPQCEVCGSNPKITDLFADYAVSTGCRSDDKILVPHLLGPNELVSVVEYQKIQNSQTKHFLLDVRQPHQFKICSLAHACNIPLDKIES
+
+>Am_tu_Hpap_XX_Contig_6949_Len544_Cov2_OG5_126966
+IQITMSNSPPPAQPNDPFDRQRYMPGFDHSKIENQVAFVMGTGGLGCSVSFALARLGVKKLFLLDHDVVDFSNLNRQILFSTESVGQKKVHAAAQGLKAHIVGDTQVEVLDMDILKNWSTAVNIAKQCTVLFNNIDIGHYFDFAVLSLGKSLGIPVVAGSSYARTWIVEYYSGKPGKSSFS
+
+>Sr_ci_Ptet_XX_001449230_Contig_21035_Len978_OG5_126966
+MDSQTIFSRQVTIEDWKQDKLSQQIVLILGVGGIGSVATTNLLRLGVKKIFLVDYDHVELHNLNRQILYSNKDVNQQKVKAAFENATFHNVGNAEIQMFDLDAVKNWDKIVELASQSTAIFNCIDYGDYWDAAVQSLCLYYKIPMIIAGSFAQSFMAELYLGTPCYACMTDGLKEEYLNQITQENITQLKDISFLPANNKPQGQSHQVLCSTAGNFATQLLLNYLNEQADSQTSKKVLFYLTTFEVVIFPVFSKNNCHICKYQEPAKEQQIQATEPAKEQQIQATEPEKEKLVQVPEPEKEQLIQATETEKEQQEQATESIQKQN
+
+>Sr_ci_Ptet_XX_001423300_Contig_16062_Len1230_OG5_126966
+MKEYIEYLQNLLKQNKIEFEQEEDFIQHKVSQINNEFGYEHINRYKRQMILSEIGLTGQKQIHLAKVLIVGAGGIGAPAIYYLAGAGVGTIGLVDGDSVDVSNLHRQIIHNNYRQGMNKCESAKLQINEFNPLVNVITYKHHLSSANAIEIFQNYDVILDATDNPATRYLINDTAIYLNKPLVSGSSVGWEGQITVYGMQGPCYRCLFPQCPKTVQNCNEAGVFGVMPGLIGLIEALQAIKIIIGQQTLSQKMILIDGLRDVYKVVKLRGQQKDCIACQKQIKINDYDYASFAQTICSSSIPYRGGYKEIEWKDFLQIQRSEKVALLDVRPSSQYNIIKLDGFTNLPYSQIDQLQVEEYKDKEIYIMCRRGNNSRLACEYLKDKTPNIYNIIGGIDLYAKLYDPKMPLL
+
+>Ba_ba_Bcae_XX_065538746_Contig_2453_Len693_OG5_126966
+MRYDRQIILPEVGEEGQKKLQEAKVLIVGVGGLGSPIALYLSGAGVGCLGLVDDDLVSVTNLQRQVLYSEKELGKPKAICAAERLSALNSEIEIHPYAARLTKDNAYDIIQEYDIVVDGCDNFATRYLINDICIEQKKPYVYGAICGFEGQVSVFNYGNQKKNYRDLYPDEEEMQRMPPPPKGVMGVTPAIVGSIEATEILKIICGFGDVLAGELWTIDLRTLQSNKFSL
+
+>Am_tu_He47_XX_Am_tu_He47-LKH612_16834_Len300_Cov2_OG5_126966
+QLPRKAAVFQDEILRSSRQLVLPELGVHRHVLVVGCGGLRCPLAQYLAAASVGRLGLVDYDVVEMSNLAYQVLHGEALAAQAKAASAAASLRGLNLAVE
+
+>Am_tu_He47_XX_Am_tu_He47-LKH612_38936_Len381_Cov2_OG5_126966
+TRYDNQISIFGKAFQEKLGKQNWFMVGCGALGCEYLKGFSLMGLGAQGGILYVTDMDTIEVSNLSRQFLFRRNNVGQQKSVCAAKAALQMNPKMNIKCFEIPVGPDTENFFNDKFWSNLDGVCNALD
+
+>Sr_rh_Blon_XX_Contig_2923_Len1284_Cov14_OG5_126966
+RKEERWPKDSDEYKAGNSRKNRVKPPPAEVEGDVFDRQRVIVGFNQGLIESQTCFVLGTGGIGQDVALTLARLGVGKIIMLDCDTYDASNLTRQCLGSIEDVGKRKVDAAASNIKAHNIRSQIETVHVDALANWNKVVEIARKCDVIFNGIDLGPMWDFCACSLAKELRIPYIAGQSYDWIFNVEYYSGDPANLCAWCAEAKSESDWISGQFNTHFGLGGDLKYIKERLKAFGEKHKHNSYDAKCITEFLKADKQKFRMDGPTVSVLVNECFEKIGGCAKIGLDDLDKFLGALMHAVVKRLLPGRITKLKEVQFIPHPKHVATRFVGSWVCPCLAAGVLMVSQFANALTGRKDSGAKDPPCNITFDLGWGQTIEEKGHQETARMVQQGIFPADSLSTITEERPRASNPAKKCCMLCTEACKVQPDTQ
+
+>Op_me_Bplu_XX_Contig_9798_Len1209_Cov295.25062034739454_OG5_126966
+MDVLGDYYNCQLSNDEIIRYSRHMLVSGFGGSDGQLKIKNSKVLVIGAGGLGCPVAYNLVSSGIGVLGIVDYDVIEIHNLIRQHLYTVEDIGKYKVECMFNVLQKLNKFVKINKYNIKITKENASDIIMCYDLVVDCTDNVETRYLINDSCVKLNKILVSGAATRWEGQLTVYNYMHGPCMRCIFPNPPDPRTVVSCDEGGIICPVTFIIGGLQSLEVLKIILKKDDILSEIMLIFSGETSSFKRIKLRSKLSECFCSGNDLVLSEFSGSCDLQTSCDKINVQEFSQILVEKVEHHLIDVRDSYEYSICSFKHSINISYLELESKYYTVEKLRSLLDSNIKNNESIKPMLIIVVCQKGNLSRRVYSILKSYLEKIYSNFNLMNLEGGLQRWHEQIDNNFPTY
+
+>Za_et_Tkod_XX_011251067_Contig_1160_Len699_OG5_126966
+MLTERELERYDRQIMIFGEEGQEKLKGAKVAVVGVGGLGSPVAYYLAAAGIGTVLLIDEQTPELSNLNRQILHWEEDVGRRSKPESAKWKLERFNSDIKIEAYTGRLTAENIDEVLKDVDIVVDCLDNFQTRYLLDEYVHRKRIPLVHGAVEGMHGQVTTIVPGITKSLREIFPKVREKEEKFPIIGATAGVVGSIQAMEVIKLLTGIGEPLLNKLLLIDLAMNIFEVVELK
+
+>Za_as_Loki_XX_KKK45330_Contig_2173_Len813_OG5_126966
+MELTEEQIERYSRQLVLKEFSGEGQKKLLESRVTVIGCGGLGSPIAYYLTAAGIGTLRLIDFDKVDRSNLHRQILHFENDIGKLKTQSAYEKLHQLNPDVNIEKVNEILQPSNIKQIFKDSDYIIDGSDNIPTKMMINDACVNLNIPFTIAGVIRFNGQILTVIPEEKTTCYRCVFGDVTEHEPSMSCSQAGVIGLIPGIIGCIQANEAIKYLLNIGDLIVNRMLFLDLLKYRFSFLKVLRNEECLACGDNPKDLIETQDYKIEDACREG
+
+>Ba_cy_Smaj_XX_072622368_Contig_1240_Len1173_OG5_126966
+MLNPNLDDIQLSKDDYERYARHIILPEVGLEGQKRLKAASVLCIGTGGLGSPLLLYLAAAGIGRIGIVDFDVVDHSNLQRQVIHGTSWVGKPKIESAKHRILEINPTCQVDLYNTRLSSENALDIFRPYDVVIDGTDNFPTRYLTNDACVLLDKPNVYGSIFRFEGQATVFNYEGGPNYRDLYPEPPPPGMVPSCAEGGVLGVLPGIIGVIQATEAIKIILGSNTTLSGRLLLYNALEMSFRELKLRPNPVRPVIEKLIDYEQFCGIPQAQAEAEQEKAAMQEMTVTELKALLDSDAQDYVLIDVRNPNEYEIAQIPGAVLIPLPDIEQGPGVEKVKAVLNGHRLIAHCKMGGRSATAIRILKEHGIDGTNVVGGITAWSQEVDSSVPQY
+
+>Am_ar_Mabd_XX_Contig_28909_Len360_Cov5_OG5_126966
+DNVELGNLHRQVIHDEARIGINKAESAACSVRKLNSSVEVIAYPFRVTPANALDIIRQYDVVIDATDNAVVRYIINDACVVAGKPMVSGAALRMDGQCHVYNFPPSKGPCYRCHNPVPPP
+
+>Sr_di_Smic_XX_OLQ02585_Contig_8528_Len3426_OG5_126966
+MRRQRTSSASDSKSQAKASTTFEEPVVESDHDDKVSFKEIMEKISEATSRRPSQYTAKVLPGVLPFGAWDTDSGEDEDKLPRRQTSSAASPEEEAASLSKSTRPIAPQPVQPPNPSDLHWATWSKACRPFTPSTEVGTLKPKQLNLWEEERVFSPSRTWPAGPLRCAAREFYDDQRRGLPAWQAVSWKHTGPSFPVPPRLRRPGSANAVGSVRKPAHDNRGRAHFRGYVRKDEAWPEDSPEYKAGNEIENRKRPPPEEVPGDAFDRQRVIPGFDQGLIERQVCLVLGAGGIGQNVAMTLARLGVQRIILVDNDVYAASNLTRQCLGGKADVGKRKVDVAKAGLDTHNLRSEVTAVHCDALSEWPKIVELARESTVVFNAIDVGVMWDYCVNSLCKELRIPLCAGQSFGWKFMTELYTGRPQEVCAFCYDSVASTFGAAKSAVERPNGLLSRLCATVKVNEDVGAGALEAFLATDRQFRCTRGPQLSSLVRQALAKMEQNSLRYGSLAEDFLSFLRAFQEETVFLLQPGRVSSLQEVTFVPRPKHAETRYVGSWVCPCLSCAVTMVSQWAALLTAPVEEFLVKTAIPQTVTFNLDNGMTGDEQLGYEFGALGMPLDKAERRFCQDACNSKCDVCASATMLAAEESLFVGCLPVTLAPVPGIVQDAPRSWLPPEGAESSARNAATKEVLLRKGPLIHLGEDYSEVVVPAMPALDWRAELSEVHRSWAPEIYAMPLLKVSGSGEEAKAPSALQGVASGIRSALVKARGRWFRLKGCGNRDEGFLVEKKGDKGEQTLRGCCFKHTADTELRMTELVCQVLGSARLDCANSSMGCYRYEQKPGWPLPKIPRYCAVFETKSNARLGDHLLGGLLSLLPHMLLDGFEHLEQCLLRGRGEESGELLETADLVCCGMATADVLAQLQQAKRSLPERPPPSSSAVPAVPTAVASLWDAVCASLAQGLRTLSSDEPSVILWLVWRLGWECGATLRALHASGIAWGTYPDSLGIHCNAHSNNFAVKPPGCGHQETFLAALDFDMAFTRENFLPEACESGALGLESFDGILAFEANMGLKTVLSGSDFSNTGVQNAQAPPSHKLLELAIRDTMVTACSEALAGSCDPHPYSAGLKAVAYDVIKLSLCLTTEVEG
+
+>Sr_di_Smic_XX_OLQ03449_Contig_683_Len10029_OG5_126966
+MNARSRKTWCFGDCFDAFRRFVGKECDAELWAGCGLTRGEVGQYGRQLVLPKLGPEGQREISRGSVLIVGAGGLGCPVAMYLAAAGVGRLAIVDGDHVEESNLHRQIGHPWRNVDKSTAGKTCLRDLLGILMPAMPCEWAQLSSEFQNLDVVALQGLCVKADSDVPCAYFRTSHHHVFQWGYTKGRYTNKSCGVAILLRHKRLRLQWVREVYSPPDQLAGRAGALRIKGRCSDLLVIVGYVPVEPTNASQRQAVHAFYTWVDSLLSRSPARTLPILLLDANGRMGLQRLGDGPGQIAADHDATVGPWGAEAQNHNGTQLRNLLHTHHLAAANTHFSRGCGATYHGPLGHPSRIDYVVVPQGLLQHITDVRVWYRSGYRLQLIDSPDLRDHCPIVVDFNYELSFPQPQRSAKWDFTKLGRAVDGHSSKEDFLRDVQTSLAALPQPSDDVCASWNALNTIVCRLARRFFTQSGSRRTQRPLDTQQAAEQTMLAREDYRDACLQLRRQQQPAQSVHLAWAAWQKYLHFKSLQRHSKQLCRRDRRHKVDDLVQQLQQAARDKNPSLQWKLAYQIAGGKHGPKKRRYDHPQRYRATAQEWVDELSLAGPQGGCAATRLDKASADAIFPFVFARGKLLPKDAVSQAALPETDMLQYDGTDGRLRRAQPARVGVHARQSAQEDLGKLREAVRTLQRQRAVPDWCAPAEVWRMLLFPSEHCDRGASLSSQFHGQVEARLLHTLVQARASQRVPTLWNISCPVELDKRNNKPGCSGKRLIHLLCPVGKAYFHQLWARTVPRYAHHACGFVRHRRREQAITQQRCINWRLQHAGLGHVTVLYDVKNAFPSPSHASLDAAVRQHARPDDVELLMQRHREAFILLRDPFQPTYTILQVGCGNMQGDRMAPSQFLSVYLPAVEEWHVACKVLPHGAALLATDPVSGQRCDTSLSTFADDVAKTHAIPTAPEFAPIVTRMDADLDRSLQGLGMAQNHDKKELLVRLMGSGAQKAMQDIYHARTAVRGQFKRVAKYLGGWMHHSCATSPEISQRIAAAKRSWSVLQGFWFRRDAPRAQRQLVFKAMVLSAVYSGLDAVPSHKGDDKRITQLLVSLSRKLLQGRACTKPWHDVREHHRSWTNLQVFQEVGLFASATERCVRRLLWWQNIVKRPDENVALLASLFGQFPWESYTQLGPDGRLTQHANPWIRQLVEDLHELCRFDLPAPGLVHDRPLLLFSAPHQAVFLSLQIRKLFKQAPAVPLEQGADGSLESADHATDSGADAVAPAPQFACGFVGPDGVACQYVASSTVALSTHRHRAHGIFIMARQMVVCNQCPWCRKVFASVEIARRHVHARVAKGACPRTGGGATSYLECLRPPERLECPICLHHASDLVALHQHVVQHVARGQGVMQQYFRPAQPARLCSSKEQEQLLKAVAKLRTRAAGKNHTLGQPSSWLWAALMKVLAMDENISEEKRQQVKSYGDAVSDPCSLSQTVLYCRISKVYDQSKVRLQVAVTPELQEFLTELQRGLEANGGERKFGPPLRGALERHVQELLGENSGKAVSLAETCRERNPNICVEAHVKRIVGTEEAVFLMQSYDVIVDCTDAPRIRYLLNDAAVAAGKPLVAASSVALYGQLAIYNFEGGACLRSESGVLGPVVGVIGSMAALEVMKVLAKSSPLHSSCLRGKMLCYDATNISQPTYMVNLSSAAAGGANDASQRTLPPEGCIPYMAGDASNSMSASELRARLLAKIPTLLLDVRQPSHFAVCRLQGAHNWPLRKIKFSDDKECLEKISELLPKPSADCEVVCVCRRGNDSLKAVHLLRALGVQAWNLQVGAPQPAAGSPSSDIRMVGGCLYILGYSLDRLYVNMGTIPYLELLATAGHDTTARRWLCGGKKQGGPAQSCTDNRQGIASRFGEDCAGSSGGGALGSQGEGHAQVRLDTDVQRKTAGCPAAAAPAAAAMAEFAATEDALEDAVGKARSQVLPLAAGDVTNIEAMDTTPSPEQLSGEGSSPAVLPQLLPATPMEAALSVTPRLLKAQALWARLFCNPSFTFAEKQQFVFSSRFRKKAVDCRHSMIEPAPRPPTVAPRPLLEQTLIWSPKSPQMAVSGHRLFPFCGTPAMVGSPHPTTAVIAFHDTRRQYAAVGRAACNFSFNTLFAGREPSQVDLRAGEACPRRPSESEEVAEQGLDHWIFRRIKKGPSRGGQEDQVGAAFDPRAHAEVQFVGSDGLYRQVPQATQAAAARRLAAATAARCQATATKPTAACSASHGLVISTTITTTITVIISTITSTIVIVMVIVIVIIIIIIIIIVNTITIITIITIITITTNIAITITTTITIIVIIIATIAPAATSEADPGDTVSGLGGDDDRNDADDRGVHDNEHGVAAMFGCKFVYHKTSMGFLNRLEVEEFLARHVQAVQGRTPSRLLYLKGFFGKRCAGDGNEDGARANIAVPESPDRELCSSAIALCSTPRPLHRCFTRKSVSVTLMRRDGTDWVGVAEAAAASFAPRFRAVWVGPSDAGEKRPNAGKDIPPCHPFLLLLLLLLLFLLFLLLILSLHSSSSDSCSDSCYCPVLGQILTADPVHATPTRAPSANSRGAERTYDAPKAGGRPPPVEDDCAEYSDRFLPGYEKTQLLGRGACAVGSNSDRVAIARRGQAAQPPPVEDDCAEYSDRFLPGYEKTQLLGRGACAVGPEFSQVVWLAVPSGSRTPVAIKQVAKGTTGKKKSDTDVSRRERAARKEILFGSYFFEAGGEPKVSPKQNPGIAHIAKLLDYVETKRDIWMVMEFGGTSLTKMAAGLQAGAYEIKGEFHRGERLYKEHRVVHSDIKPDNILIDEDDRGHIRARFIDLGSAFSFDAPSTGLTRLKRWSLGSILLEMGLGTPLCRVASDQRNNAAGLGLFAVPGRDPEKILLRQADAICQRGLAAVLRGAPGVPLEGTERTTRPGCHGRAGCGGSFDTAACAYSGDSTGCDALAGDGGSRLVVITIITIITIITIITIAITIIIFIIVVITVLIPGGGGEFNGLDLLERMMDSNSEVKCLELRSWGTTLYPLCGIDPNALSFEDAGERRTLLCLVIEEAVKLNNDLSKVDLLLEARADPCRRSETGSFPLMLAAHHSNLKLARKLLQARAEINQQDTRLVTPLHAAVHEDSAQTVQLLLMHKANVNAQDQVGQTPAFFAGSTTVIAALVDAKADLHHLNKKGQSALHLAAHNGRYEAVVYFTDHEFLAETVDMQDERGRSALHMAAVRGHQRVVSRLMDVGANPRLKMQNGQTPMTLADKKDTDLALYIYTRMTGSKHATWSETAQNPMYLGCIFGLVPAVNIIREVGAKAWQFWGCVLPFVAKLDSPSNRWEAND
+
+>Za_eh_Hvol_XX_004044375_Contig_1819_Len813_OG5_126966
+MTLSLDATQLDRYSRHIIMDEVGPEGQGRLLSSRVVVVGAGGLGAPAIQYLAAVGVGELVVVDDDVVERSNLQRQVVHCDDDVGTPKAESAAAFVRGLNPDVSVEPVEARVDKSNVHEVVAGSDVVVDASDNFPTRYLLNDVCRFEGIPLVHGAIYKFEGQATTLVPDGPCYRCLFPEAPEPGTVPDCATTGVLGVLPGTVGCIQATEAMKLLLDEGEALDGRLLFYDAMDMTFETVPYRTNPDCPVCGEGGVDSIEDIDYVESCAISLD
+
+>Ex_eu_Egym_XX_Contig_52399_Len342_Cov3_OG5_126966
+WKHDLIEQQVALVLGAGGVGSGVAMALCRLGIRKLFILDFDDVDPTNLNRQVLFSKSNIGQLKVHAAAQALQGLHNLRTEIIPLNMDAVHRWHDVVQVAQECTVIFNGIDYGEW
--- a/PTL2/Data/Pre-Guidance/OG5_127020_preguidance.faa
+++ b/PTL2/Data/Pre-Guidance/OG5_127020_preguidance.faa
@ -0,0 +1,47 @@
+>Ba_ac_Srap_XX_020872230_Contig_8017_Len465_OG5_127020
+VKLDSMYQDVILDHYKNPHGRGLRNGDAEVHHVNPTCGDEITLRVRLDGDTIKDVSYEGQGCSISQASASVLNELLVGKELAEARRIQETFLELMQSKGKAEPDDAMEEVLEDAIAFAGVSKYPARVKCALLSWMAWKDATAQALGETAGGKTA
+
+>Sr_st_Pinf_XX_002907422_Contig_14057_Len477_OG5_127020
+MIARTALKRSMGVFSRPAANVTAPAFTRARMYHDNVIDHYENPRNVGAMDKSAKDVGTGLVGAPACGDVMKLQIQVDENGTIVDSKFKTFGCGSAIASSSVATEWLKGKSVEECLQIKNTDIASHLKLPPVKLHCSMLAEDAIKAAISDYKRKQSASG
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_9898_Len561_Cov20_OG5_127020
+STQSTGALAIMSAVFLRHFIKKATTIPKARVVPPLQQVSGREYDEKVVEHFNNPRNVGTMDVNDENVGTGLVGAPACGDVMRFQFKVDENGKIVDSCFKTFGCGSAIASSSFATEKIVGMHIDDAAKLTNKDIAKELNLPPVKLHCSMLAEDGIKAAIKDLEQKKAAKKTGQQSPAKQSKVGDKQP
+
+>Am_tu_Hpap_XX_Contig_8637_Len346_Cov6_OG5_127020
+YHERVIDHYENPRNIGKFTKEEEKSGLVGTGLVGAPACGDVMRLQLKINNNIVEDAKFKTFGCGSAIASSSLATEWVKGKTVEECLEIKNTEIAQHLALPPVKLHCSMLAEDAIR
+
+>Sr_ci_Ptet_XX_001442921_Contig_33785_Len450_OG5_127020
+MLTLLKRSIYFVPRFSYHPNVIDHYEHPRNVGSLDKSNPKVGTGLVGAPACGDVMKLQIQVGEDGKTIEQAVFKTFGCGSAIASSSYATEILKGMTLEDAYNIKNSDIASYLKLPPVKLHCSMLAEDAIKKAIEDLQSKNNQSTQKQDK
+
+>Sr_st_Bhom_XX_012894290_Contig_4785_Len453_OG5_127020
+MFSLARSAPRFVFAARSLTCTTRLYHDLVIDHYEHPRNVGSFDANDDDIGTGIAGAPACGDVMKLQIKVADGKIVDAKFKTFGCGSAIASSSVASEWVKGKTLEEAMTIKNTDISNHLKLPPVKLHCSLLAEDAIKAAVNDYVKKSEKKQ
+
+>Am_tu_He47_XX_Am_tu_He47-LKH612_46933_Len207_Cov4_OG5_127020
+CGSAIASSSLATEWVKGKTVEECLEIKNTEIAQHLALPPVKLHCSMLAEDAIRAAIRDYQKQNVSTDN
+
+>Sr_rh_Blon_XX_Contig_13018_Len525_Cov130_OG5_127020
+MLRGLCRSVRFNAAVISRRMYHPNVVDHYENPRNVGSLDDKDENVGTGLVGAPACGDVMKLQIKIDEEGKIEEAKFKTFGCGSAIASRFKNYYFKNIFSILNYFQIIFSTSSYATEWLKGKQVDEAAKLENSEIASHLNLPPVKLHCSMLAQDAVKAAIKNYKEKKGLTESESS
+
+>Op_me_Bplu_XX_Contig_17337_Len486_Cov11_OG5_127020
+MMALARFANVGSTLCKSLPNLVTAAPKRAYHEKVIDHYENPRNVGSLKKDESNVGTGLVGAPACGDVMRLQIKVDENGKIIDAKFKTFGCGSAIASSSLATEWIKGKTTDEALRIRNTDIAKELCLPPVKLHCSMLAEDAIKAAVVDYAAKKKQAASASGS
+
+>Za_as_Loki_XX_KKK44574_Contig_2174_Len813_OG5_127020
+MNKLKSTQYTEKVLDHFRNPRNVGVIEKPDGEGKVGNPVCGDLMLITIKVAKGDKDEEDIIEDIKFQTFGCGSAVATSSMVTTMAKGMKVNDAYEISRKDVAEELDGLPPIKMHCSNLAADALKAAIDNYRGKAETYVGVEYRTCEASELKIILGIDEFLGKGVYKKKVEDLSEFNNKRVFVIDTGDESLEYALELTNHTGRVIVVTSAKSVPGPENLRRKIKRSDVKMIHQSELLEVLGTNDVEKVKIHDFDEDENYELFIDVVIILEE
+
+>Ba_cd_Cavi_XX_038500876_Contig_444_Len822_OG5_127020
+MTVPFQPTASWTYISPKVMKTFHKFYCAGVFSTEDAEIKNAHLVIGNQGHRLMGNLVVFYWLVDKTNGKILDAKFQYFGHPFLLVLAETTCNLVTGKTYAQAYNLSVNDIDTELRSHKEVPALPELYAPLYHCIIDALDVAAQQCMDISVEDGSLPLNNALLTHDFENANPFTQEEWETLSLEAKLQTLRSVTEEKIAPYIALDSGGVTIEHLEGNVVTISYTGNCSGCFSAIGSTLNSIGELLRAYVYGELQIKVNEASLDFSQSHHSNIDY
+
+>Am_ar_Mabd_XX_Contig_6437_Len1017_Cov32_OG5_127020
+LGKTGLVGKPLWAQYSAKVRDRMDNPKRRGAITKEEAAAMNCDLVVAEHGAEACGDAVRMYWAIDKDTRRIKDAKFQSFGCATAIASSDITAELCIGKTPEEAEKLVTNLEVEKALRDTPDKPAVPPQKMHCSVMAHDVVHKAATSVSLPTSAAAALANNIKNEDDEIVCECARVTLGSLRNAIRTNKLKTIADVTHYTKAGGFCKSCIKPGGHEARKRHLVDILREEIKKAGDQPSTMTVSKLKGKSLAAKAAMVQKAIDKEIAEALGSHGGSVELLDVEDGKDGVFVVYVAFLGQCAGCPSSTNQTLSFIESKLKEVLGESDLVVKVPQNNLDGVY
+
+>Sr_di_Smic_XX_OLQ05395_Contig_19472_Len1671_OG5_127020
+MLPQLFPTRCRGPGRLQDLARFLIRRGLPFPRSPEIMSLSILSRRAAAPLFAPRFAVAARRGYHEVVHDHFNNPRNVGSLDKEDKSVGSALVGKASCGDVIKLQVKVGEDGTIQDAKFKTFGCGSATEMIIGQNITEASKITNSDISSHLKLPPVKIHCSVLAEEAIQAAIADYKTKNSSEEQVSYCLALRNNRGAGDVNVPCSRSLQRLPVSKSPEIMSLSILSRRPAAPLFAPRFAVAARRGYHEVVHDHFNNPRNVGSLDKEDKSVGSALVGKASCGDVIKLQVKVGEDGTIQDAKFKTFGCGSAIASSSYATEMIIGQNITEASKITNSDISSHLKLPPVKIHCSVLAEEAIQAAIADYKTKNSSEEQVSYCLALRNNRGAGDVNVPCSRSLQRLPVSKSPEIMSLSILSRRSAAPLFAPRFAVAARRGYHEVVHDHFNNPRNVGSLDKEDKSVGSALVGKASCGDVIKLQVKVGEDGTIQDAKFKTFGCGSATEMIIGQNITEASKITNSDISSHLKLPPVKIHCSVLAEEAIQAAIADYMTKNSSEASAL
+
+>Pl_gr_Dsal_XX_BM448698_Contig_846_Len504_OG5_127020
+MLPIAALVRLTPLARPTVANTALPLQQQFARGYHENVVDHYENPRNIGALNKSDQDVGTGLVGAPACGDVMKLQVKVDENGYITDSRFKTFGCGSAIASSSVVTEWIKGKPLDEVVKIKNSEIAKHLSLPPVKLHCSMLAEDAIKAAVKDIQAKRAASAKPAAEAKA
+
+>Za_eh_Hvol_XX_004045199_Contig_2957_Len429_OG5_127020
+MGIGSDMYRQQIMDHYKNPRNHGRLESPTFTHTGENPSCGDTITMDVQLADDGETIERVAFSGDGCAISQASASMLTQRLPGTTLSELEAMDTDDITEMLGVDISPMRIKCAVLARQVAQDGAKIHDGEIEIEKTKTEDGDD
+
+>Ex_eu_Egym_XX_Contig_18068_Len399_Cov178_OG5_127020
+YSDLLVDHYENPRNVGSMDVHDPTVGTGLVGAPACGDVMKLQLKVDHNGIITDTAFKTFGCGAAIASSSLATEHLKGKTLEEAAMLTNKEIAAELLLPPVKLHCSMLAEEAVKAAVKNLQAKRLSPAKVEVI
--- a/PTL2/Data/Pre-Guidance/OG5_127169_preguidance.faa
+++ b/PTL2/Data/Pre-Guidance/OG5_127169_preguidance.faa
@ -0,0 +1,65 @@
+>Sr_st_Pinf_XX_002901673_Contig_13960_Len483_OG5_127169
+MALRVISQTLRARALKSATSAAWRANSQRPAGFAFFSTKYTPQHEYVTLNGKEGTIGITDFAQNSLGDVVYVDLPSVGDKFAKGDAFGAVESVKAASDLYTPAAGTVTAVNEDLAESPNLVNDEAMTGGWFIKLELDDVSDVDDLLDEAAYKEHCENEDH
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_10569_Len456_Cov26_OG5_127169
+MRVPLRKLTQSLSRPSLMISNVQYRHFSDYRYSEDHEWLKIEGDEAVIGISDYAQESLGEIVFVEFPEINDEFGKGDVFGQVESVKAASELYMPVAGTIVKVNERLSDEPGLVNSSPETDGWMIRIKMKDTAEADELMDATKYGEFTENLH
+
+>Sr_ci_Ptet_XX_001427238_Contig_32911_Len483_OG5_127169
+MLSRGTSYDYFVQIFNINIFLFKMYMRSIFKLRQAFSVLTKYTKDHEWIKYDTQTKIAKIGITDYAQNELGDIVHVDFQKVGLLFKTHQSLGAIESVKVAADIYAPVAGEIVGINEDLKDSPNLINEKAEETWILQAKVQNESELDTLLDKQSYEKIINK
+
+>Sr_st_Bhom_XX_012895318_Contig_4060_Len594_OG5_127169
+MVFIYGGFQVIFEWFIHSYYVLSMDFLGYVDFSRCSSLACRFNDSTILLFEASSRFASKTLTSARFLASRSFATYFSKDHEWIEYTAGKPAVVGITDYAQHSLGDIVYIELPEVGSTIKAGDSFSSVESVKAASDAFCPATGKVLEVNTVLSETPSLVNESPMEKGWFMKLELSNPDELKELMDKAAYDKFCKEAEH
+
+>Ba_ba_Bcae_XX_065539607_Contig_3228_Len381_OG5_127169
+MNFPQNLKYTSEHEWIRIEGDIAYVGITDYAQEQLGDIVFVDIPTVGETLEAGETFGTIEVVKTISDLFLPVAGEVLEQNEALEENPELVNKDPYGEGWLIKMKPADPKAVEDLLDAEAYKAVVNG
+
+>Am_tu_He47_XX_Am_tu_He47-LKH612_22114_Len465_Cov3_OG5_127169
+MSRLAVKSFVSVSKLALRSKTSFSRMSSTLRFSPSHEYIRLEGDVGTVGITDHAASALGDVVFVDLPSVGASYNAGDSFGSVESVKAASDVYAPVSGVVLAVNSELETTPSKVNESALSAGWFIKLKVSAKGKAEFDKLLDEAAYKKHCDEEKH
+
+>Sr_rh_Blon_XX_Contig_11807_Len363_Cov26_OG5_127169
+MWVQRLSTGLYRVGVTKKLTDSLGGIGFVDICAEGSILTSGKPFGMVEGPSGTFTVSSPISGEVIECNEILKKNPTVVLSFFIKCILLPSNEMITTTTEFIAALIYCISLHRENKRCVTF
+
+>Sr_rh_Blon_XX_Contig_15350_Len435_Cov131_OG5_127169
+FARSLVSRLSATRSFAVRRVPFSTLYTKEHEYLKADGDLHFMGISDHAQSELGDVVFVELPEVGAEFAKGDALGSVESVKAASSVYAPIDCEIVEVNKSLEDNHGLVNESAEEDGWMVKLKATNPDQLSDLLDADTYATFCNEE
+
+>Op_me_Bplu_XX_Contig_33079_Len183_Cov7_OG5_127169
+SLPLSSAPGVRYISLTSRALGDRRFTAKHEYVDISGTVGTVGITDFAQKELGDVVFVELPA
+
+>Op_me_Bplu_XX_Contig_24111_Len219_Cov9_OG5_127169
+TMESVKAVAEVYSPVAGVVREANAALSKQPGLVNTSPYDEGWLVKLDLTQQQVDAAAQLMDAAAYEKYLKDH
+
+>Za_et_Tkod_XX_011249105_Contig_1767_Len405_OG5_127169
+MIEVGEYKVKEGLYYTKDHEWAQVLDDGTVLVGISDYAQKELGDLAYVELPEVGKEVSKGDVLCEIESVKAVSEVYAPVSGEVIEVNEALEDSPELLNEDPYENWIAKLKPTNLEEELKELMDAQAYAEYLRSL
+
+>Za_as_Loki_XX_KKK41499_Contig_3774_Len426_OG5_127169
+MKGIEKREKKMDYEFPSDIKYTTTHEWVKIEDHITISGITDYAQHQLGDIVFIELPEVAMVFERENNIGEIESVKAVEEFLMPLSGEIIEINNQLSENPELVNTSPFRDGWLVKIKISNENELDELLSVEKYKELVKSEEQ
+
+>Za_as_Loki_XX_KKK43764_Contig_3936_Len393_OG5_127169
+MTKWFTKTHQWFDDGTKEVGITPYAADQLGEISFVDVEGLEGAELEQVTMDGDEPTSDPIDCTVESSKAVGDIYSPVSGTVTELNTKLMDEPEKINEDAFTAWLYKIEPSNWDADKGNLIDESAYNAFIG
+
+>Ba_cd_Cavi_XX_038500181_Contig_758_Len342_OG5_127169
+MWYSSYHVWILPIHESIVRLGVTKRMCSNLGEILHIDLPVLGNVCKEGEVLVVLESSKSAVEVLSPVSGKIIEVNQGLMEDIKLLNTSPEDLGWFVVVDLGRPLNTENLLAKD
+
+>Ba_cy_Smaj_XX_072619214_Contig_3382_Len399_OG5_127169
+MAFEYPEDLKYLDSHEYVRLDGEIATIGITSFALDQLGDIVFLELPEMGDDVEAGEGFGTIESVKAVEDLKAPISGTVIDRNEGLIDAPESLAEDPYGEGWLIKIRIADPDGDLEDVLTAAEYKAQVEGDEE
+
+>Am_ar_Mabd_XX_Contig_34632_Len264_Cov5_OG5_127169
+LKYTNDHEWIRVEGNIGTIGITAHAAGELGDVVYIDIADDLTEMTSGENFGTIEAVKTVADLLAPVTGKVTAINTALNDAPETVNNDP
+
+>Am_ar_Mabd_XX_Contig_17937_Len387_Cov34_OG5_127169
+RYAKTHEWVCAEPGTRNIAKVGISDHAQKLLGDLVFVEVPPVGTSKAKGATLCVVESVKSVSDVYAPVSCEVVEKNEALKDPTLLNKDAEGKGWIAKVKLTKLDEFESLLDEEAYKKHCAAEEAAGHH
+
+>Am_ar_Mabd_XX_Contig_10872_Len312_Cov4_OG5_127169
+IPKGLYFGKTHSWAFMKKNGSVKIGIDDFLQHVTGKITRVELKRAGETVKKGELLMSIIRKGKLLNIYSPISGTITEVNENLESNSSLLNSSPYSEGWVYLIEP
+
+>Sr_di_Smic_XX_OLQ06495_Contig_4103_Len5250_OG5_127169
+MFRALLCTALLVQTRSWECPAGFAGPEKCLGKENAGKCELQKPSKVDIDTNNALSCGNPNAKLAEFETDLGGGSYYKGCGLNQDGLVDSCCNCWPLKEAASNEVKIVPISNAEDRPSAFDDDPACDATSQQDTDVQEAPQQFRMALTSAACVTSTGLGEWVITRFWSPGHLENLECHFFRNFANSPLPGYIEVQALAVDRRSIRRLDRFSICPRLLSPLRAVMSSTGAGFVDVVVADLVAPPTSKSATSASPLEASPAPGEIGENAGQPTMGAQAGGIAGSPSTGTSALVETAVADEDPVMGVPPSSDEEEELLADVVGAQHFPGVDVVDGEAQTVHFTPILAFDAHDVGVQTANEVMFSSFVGDIVCRRPPATDFAIPAGRQGGPGGLWHQEPESPTAGAGTQHLGRLPVPAPRTGADLRHKEIPYSVVGWTADTWEEAERLEAAIASGASTPPQSVSAGVILRSLPPNVRGGRLPRERPADFTKWIGWCFVKCPDTVGGGLAPTTHRCWAAPTSTTSATAVHRRRRGSASTRLKFRHHGPASGLVCGARRTGRENRPVRGAALARPGWSSQHRRPHRPGRQVGGRNLALEAMLAAPPLVEESSTLALVGAGPSRPDLPVRRDATRASLAAAVEAVRPANVKRAPDLEPPGVRGQGPRLAHLYPDLSGDWRRLSGRRVPERYFLAAFRYQEHDLGIRGGIPPALAPLVNFADRAAFDPARAAHSADVFVIAVWFMLREIEVAAARVSDMVVSPGLAVRQCGTDAAPGRPGHAWASDEQEFFAGCTRPWLHGFHSPGGQRWVVCPRALRVNDRYARAASDDDPMFGCILDADIPEFEPPHRVLEWPVVPTGDYAYNAKLLDGKPRQFPTRRLAGADAVLSRIYHEHTVSKAYTPLLLGEILSARTWTSADELNKLAAGGKEPSGGALHIVAGTVVAAWEPRGVMAMPDRPRDQEHTRALLDELVAETRLGRVTRPCAAPDHWSVSTVALPSVADMGVLRQPPPGLFRGPLLRHLPGRRERRAEASPGRGLAPVRPQRHHGASDVPTHHFLDAYRQWAVRHPGHCGTFLPSAAGVTLWFHFAMCFGAAASVWNFNRAADAVQMLLRSLLLVLLGHFVDDFNGVDAADLADSAHHAVADFFALLGLQTKPSKAQAPAKRHVVQGVELSIRPEGVELSPTAQRTQKILGQIDDALARDSLSPDEASRLAGRLTFLSQSTFGATGRAAIKPLYSRAADTAANSDDTLSVGLRLVASHRPRLVPWPGRVTGPFPVLYADAFFLDGDLRKKPGHLAAGEAVPKAARWQNGCGYVLLLDGHVFYDYGVIKPEHLAPFAARKAFIYVLEIVAQVLPLVTFARRLSPFWIAFIDNVAGQFALMKGYGKDPSVNGILASFWGLASDRQWAPDFHRVPSESNVSGAISRGDDSRARAEGWTRLTTPVDDIMDVLARAASDIDFACHVQALAVDRCFIFTTFDFVNRPAPAYSGGAWGRAQKYLRREESMGIELARLTEQGQRYFTKTHEWFQVEEEGVGTVGITQVAQRALGEVLYCKLPQEGARFKVMETLATLEALKSVGEVHSPIRGEVIEVNSRLEREPALVTYAPLTDGWLVRMAFDGQIPRYLRRSSAIPRSQVEPLLADIPGLVRYLEERLLSSPGDSDALQELTFDGLRTIERWYIHKAASELNLYTASHGTGAGRQLVVRRAPRTRNQPGPDADEDSDDEEEDEEEEAIPQRERPRLERRRKRAPVRVLYK
+
+>Sr_di_Smic_XX_OLQ05697_Contig_11407_Len2760_OG5_127169
+MGWTWALFFANETVASIVRETCEGHGCEMREKLPVPQLWDSPTITSTYVDNVAIIGARKKDVENRAQRINEAFEQKGIPIVWSYTSPVRRLETVGCCIDFEKKTLENKAARLWRVYLAGLELVKRSKVRGKVVQVWLGHVTAIFRFSPYLLSIFDKIYRFTMITEDKRVSLWPAVRAEIQNACDLIWFARVDLGAGYISHVDMGDSADKGYALMSRSASTSLIRAACCFREKWRYVSLPDSLKELVEKVGVSREDVYDFGRLESTMRSTWSGATLSGVGLGTQYSQWLQEALQEGSWLKTSPLMSQYRAKRSMRVDVDCPALVPPLDPELLSEGTFKLLWAKRWKNPEEHIGMKEGRVALSSLKRSARVLSLCGKRKLTICDNLPVVIFFEKGRSSRPGPNRLCRISAAIQAIKAVLENASDKYSADAAEITWALETASSIRGSLKRLPSDSTPKRRWRQGERVDSNSNINAKPCNKKLLKKRELSVEAAVPPHKRLRASKVKPTTLKLYHNAVVEFEEWAADRALNLGSHKEIDEALVEFLHELCEDSRNISDANYTIFGYILLKSNFHMQDRDQLPFAKQAMKGWRARFPAKSRTGVDLRLWDLVALHCFRLGFIDSAAAILIQGDSYLRPNEVLSIRRDCVVPPSSSTLSEIWGVVICPFEEGVPTKSGEFDDTILFDTKERMDVNVIMKCLYRASRGHDYLFENLSYKDYVSHVKKASEHVRAQTVFTRSVISTRYKNVVGGSALSDILHPGSMAFALRASLRSACRMHGLRSGLAAPTFAAPRFGLRCFSDLRFAPTHEWFKAEGNTATLGISDFAQGQLGEVVYVELPEVGATFSTKDTICTLESVKAVGEVYAPVDMEVTDINSKLSDEPATINSSPEDEGWLVKVKFSGDASSLMDRAAYEKHLESEKTEE
+
+>Za_eh_Hvol_XX_004042292_Contig_3157_Len381_OG5_127169
+MFEIPDDRKYLESHEWTTTEGDAVKIGISDFAQDELGDVVFVELPAEGDELAAGEEFGVVESIKAVSDLYAPISGTVTAVNEELFDAPELLNDDPYGDGWMLAVEPADTSEFDDLLSPEEYREQTE
+
+>Ex_eu_Egym_XX_Contig_29495_Len522_Cov2_OG5_127169
+MLCPCRCIPRPTADQSKLMHVHARLRTVGGAQRAQALISEYQRLSGTDASAGLYYTKDHTWVRLAGTTAQFGWTQKHQRDAGEIVYVELPEVGETYEADEPVGVVESVLGAEDIMMPVSGKIREVNTLLVNSPWLINTVPESDGYIAIVDVHDPLPDGLMTKEEYHIWLESAL
--- a/PTL2/Data/Pre-Guidance/OG5_127195_preguidance.faa
+++ b/PTL2/Data/Pre-Guidance/OG5_127195_preguidance.faa
@ -0,0 +1,50 @@
+>Sr_st_Pinf_XX_002908862_Contig_8654_Len960_OG5_127195
+MLLRSSRVGINCRYLSVLSGISEDLLVSTSIGHQIGGDSHAALVDSLVQTNVVAAGSRLEAALRRVDRADFVAPAFQSSSERYANRPLKIGTVATISTPQQHAQVLGLLEPHLQPGMTAMDIGCGSGILVATMAQLVGPMGFVTGVDIVPELVEFSKENLQRSLGKDAADKQTKIIVSSGKKDLGLPSDVRYDCIHVGVAVETKAEAESFLNYLKPGGGLLIPLGGAGTEQKLVKMTKQADGTVDKRDIMSVLCQPMLDSIPVEDIQETRAENLARVENALTLWREDFETKNGRKPTRDDLMGNEESKKLFQEFASLRK
+
+>Sr_st_Pinf_XX_002899158_Contig_11057_Len720_OG5_127195
+MSFWPCNSSSNEGLVSNLKRTNVVRSDAVFNAMVKTDRAKYLAQIETPDGGHVGELAAYQDVPHPIGFHQTISAPHMHAHAMELGYAAIKDVRHPRILDVGAGSGYLTACLGRMVEDNGHVFGLEIVPGLAQFAKKNIQTADGDLVDRGVVSVRCHNGWDGLPNEAPFHYIHVGAAAESPPQALMDQLADGGRMVLPVDEPRGGQVLVEITRHGTNFSQRRLFGVCYVPLVRERERKLS
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_5949_Len699_Cov11_OG5_127195
+MAWFFRSTLKSHGELVDYLCRSNIITHKEISQAMLRVDRADFAPSHSYMDSPQYIGYNATISAPHMHAHALNDLYSNLQPGMKALDIGSGSGYLVAAMAYLVGEKGKVIGIEHIQELVDLSVVNVNKHHADLLKSGRVELLCGDGRLGYAKQAPYDAIHVGAAAAVNVADELCKQLKNGGKMVIPVELQSGEQIFREYVKDEQGKVSYTNKVAVRYVPLTNEKSQRKSGLFE
+
+>Sr_ci_Ptet_XX_001441355_Contig_27476_Len696_OG5_127195
+MNNKLEKLVQNLFKKGVIKSEIVKKVLLSVDRQQFVDESDKIYAYEDYPLQIGYNATISAPHMHAYSLELLKDHLQNGVRALDIGSGSGYLCAAMFLMMKSQQSKVIGVEHVPELVEKSIKNLSQQFKIIIDRAYNQQLKDKQIQIIRGDGRLGFEQEGPYQAIHVGAAAETIPQQLLEQLDKGGRMVIPVGKGNQVFQVIDKDQNGKINIQNVLGVRYVPLTDLNKQLNK
+
+>Am_tu_He47_XX_Am_tu_He47-LKH612_22028_Len534_Cov4_OG5_127195
+PQSIGFGATISAPHMHAMCLENLKTHLSSGKRALDVGSGSGYFTVLMAAMMSLQGVTVGIDHIPELVDMSIANIRKSYFEMLDTGRIVMIAGDGKLGAEQYAPYDVIHVGAAAAEIPKALLQQLAVGGRMVIPVGPEGEVQYLMQIDKISEDQYKETKLTGVVYVPLTSKAHQLGRA
+
+>Sr_rh_Blon_XX_Contig_11391_Len354_Cov7_OG5_127195
+EDKPRNIGCEATITSPHMHAIALEALFSEDEIETKSKNRSPEKPVIGLDIGCGSGYLTVCMGHILASDDSKVYGIDHARELIALSRNNTAKSHQNFLDSGRVAYYEGYTAFLXXXXM
+
+>Sr_rh_Blon_XX_Contig_6457_Len843_Cov9_OG5_127195
+DRGDFSFSPVHSYANLGTIFGMGPILSSPWFHFEALERIRDALQPGRKILIVGAGSGYLACIMARMVRCSGSGGHIDVMERDKSSLLSAEYNIRKNHEFLIEDRVVRMHLVDEPHMGFQQEMSNGEQEKDSGKYDAIYVTEQPDEDLTYSWELVLCRQLAENGTLIVPNFQITKDPESSDDDVVPLMQEVVPNLKRPINPRDRWTGDKEQRQRQRRDWMRDKPLLGKTAEEMEQIFKSSEDSPVKETTDGVNNTISYVNWYEKRLKDWHQKALQCHNRLV
+
+>Sr_rh_Blon_XX_Contig_8535_Len534_Cov16_OG5_127195
+STADSHEKMVSNLVKNKLIRSENVIKAMKSVDRKDFVNEKKRAYMDRAVLIGYGSQISAPHIHASGLELLATFARKGAHILDIGSGSGYISTCLARMGCSKVTGVEHVADLVKQSKQNISANHKELLETKQVKIICADARKLVGPEGCSFDAIHCGAVTTRSTVTITPSFLPSIRRN
+
+>Op_me_Bplu_XX_Contig_14799_Len678_Cov843.5132743362832_OG5_127195
+MAWRSVASTHLDFINQLRHHGVIENHIVYEIMKNVDRAEFVHINPYNDCPQAIGYGATISAPHMHAFALEYLKQNLIDGARVLDIGSGSGYLSVCFALMVSPKGKCIGIDHINQLIEKSINNTKKNHSDLLENNLLEFIEFDGRKDMSNLGKFNVIHIGAAVEELNQNLIDMLEPSGLLLAPIGEANATQSYNLVEKSKDGRTFNSRKLFDVSYIPLTDKSKQIS
+
+>Za_ec_Maeo_XX_048062537_Contig_935_Len645_OG5_127195
+IKKMEAIVKGLINAGYLKNKMVSKALLTVPRHEFIPAELHDYAYVDTPLNIGHGQTISAIHMVAIICDALDLKEGDKVLEIGTGSGYHAAVVAEIVGKNGQVITIERIPELAEKAESTLKKLGYTNVKVICGNGTLGSSEFAPYDKIYLTASGPDIPNSLIEQLKKGGKLVAPVGLYIQDLILLEKKNGNIIKKNLGAVAFVPLIGKNGWHNEY
+
+>Za_as_Loki_XX_KKK40357_Contig_2627_Len690_OG5_127195
+MIGIEMSLEDKRKSLVESLKKRDIITKSEVIRAMLTVPRHKFIPKSVESSAYIDSPLSIGKGQTISAPHMNAMMCEYLELKEGDKVLEVGTGSGYHAALCAEIVSSKDSKIPGHVYSIERHKELVESAIKSLVETGYDDRVTVIHGDGTIGYPKEAPYDKILVTAASPKKVPPPLREQLKDKGLLCIPAGSKNFGQKLYIVRKQGSDFKTKEITGVRFVPLIGKFGFEP
+
+>Am_ar_Mabd_XX_Contig_10564_Len810_Cov7_OG5_127195
+GSGKRRNAGFVETLLHRQLIRQESLLKAMLATDRKDFVAQDTDLDIVYSTEKFEALPLGWNATISAADVACVGLDLVAENLCDKPAGCRVLDVGCGSGYSTAILARIVGSGGLVVGIDHIPQLIDLAHHNISRSDPALLQHIKLVVGDGRSGVPEYAPYDAIYSAAAPESIPAELVRQLKPGGRLLTPVGPQNGMHVLTQIDADADPTNKPRITCLGTVRFVPLTDSQTQLEGKAALHVQLTPTYHPAPDTTPQQLELIKRTVLSHTKK
+
+>Sr_di_Smic_XX_OLQ08187_Contig_31007_Len810_OG5_127195
+MMPQMPLAKQVRDTHADEKTLPETAHAQKVLATRAELLRDNWPVDDDVVHAMAGVDLNAIFQCLERNRAKEPAWKPAYAKYLDDSRVAHLEQGGYVFENLSVYMVLLQLLSPALHHPGARVLDVGCGTGFLTAALATMIAERSGHVEAIDIFQRQVEHAERDIRECLPHLLPFCSFQVANGWEYRCEECFDAIAVAAQCDHPPENLVRLLKPNGILVCPVGPVVPIDSKHPGRFQPYWMVKMGPVAGAAPAFSGRAGPISVNFLPLLPP
+
+>Sr_di_Smic_XX_OLP94023_Contig_30658_Len831_OG5_127195
+MGSRAPAAEVPEEEAPVCRFCGVRLSTADSHEELTELLFRHGVLRSAKAVEAYGAVDRADFIPEDGDAYLDAAAVLGRTGAQVSAPHVHAAALELVQDKIASVHEELRILDLGSGSGCMAAMLAHLVLGHGRVLGLEHIKELADESVLNVAKNHKALLADGTLELRCQDARTLTEDENRFHIVHCGAALEGPEPWLLKLLHPGGRAVAPIGTADTPQWLSSIDVSEEGEPVVEKHLRVLYVPMTSEEDQRSRGAAWEDVVARCVRNSADLPPLDRP
+
+>Za_eh_Hvol_XX_004044448_Contig_2049_Len735_OG5_127195
+MDNSVLRDDMVDGLEHSLELLPEAVSIAMRSVPRHEFVTDSPYQNRPTEHRDTNTTILAPTTVARLLAALDPQPDDEVLVVGAGVGYTAAVLAEIVGDARVHAVDITRSLVYEARENLQRAGYGGVLVDCRDGAEGLADYAPFDRILVEASAVRPPARLLAQLADGGRLVMPKGVGEQTLVAVEDGEVAESFGPLSFKPLLVDGEQTGSIVRNRTRREDPEYEGRGWHAGHGWEQDWIDWGGSG
+
+>Ex_eu_Egym_XX_Contig_2661_Len630_Cov6_OG5_127195
+SNVELVNFLFRAGRLMNEDVKKAMLTVDRGNYCGPHDPYGDCPQSIGYNVTISAPHMHAMCLDLLKDYLKPGCRALDVGSGSGYLTACMAVMCGQAHGIEYIPELVPISIANVKKDGKSDLLDGKTLTFQHGDGSKGLPSFGPYDSIHVGAAAPQLPEALVEQLAAPGRMIVPVGPQWGAQELVVVDKDAAGNVTQRTECGVRYVPLHM
+
+>Ex_eu_Egym_XX_Contig_22233_Len759_Cov14_OG5_127195
+LPMPSHASDVAATRNELKPWPVDEDVVEAMSAVDLYKIQATLAKHRQVEPAWKTSYAKFLDDSRVAHLEAGGYVFENLSVYMTLIQLLAPAVRSTTATCARXXXXDVGCGTGFLTMVMAHLVAPNAGHVTAIDVFERQVQHAERDMRAVRPDLLPVCTFAVANAWSFQSEQKFDAIAVAAQCATVPQNLVALLKPGGRLVLPLGPVVPINSKRADKYNPYWLVEAGAEGEPPVREERAGPISVNFLPLLPVA
--- a/PTL2/Data/Raw/Am_ar_Mabd_XX_Am_ar_Mabd_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Am_ar_Mabd_XX_Am_ar_Mabd_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Am_tu_He47_XX_Am_tu_He47_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Am_tu_He47_XX_Am_tu_He47_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Am_tu_Hpap_XX_Am_tu_Hpap_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Am_tu_Hpap_XX_Am_tu_Hpap_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Ba_ac_Srap_XX_Ba_ac_Srap_Streptomyces_rapamycinicus_NRRL_5491_GCF_003675955.1_ASM367595v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Ba_ac_Srap_XX_Ba_ac_Srap_Streptomyces_rapamycinicus_NRRL_5491_GCF_003675955.1_ASM367595v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Ba_ba_Bcae_XX_Ba_ba_Bcae_Bacteroides_caecimuris_GCF_001688725.2_ASM168872v2_genomic.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Ba_ba_Bcae_XX_Ba_ba_Bcae_Bacteroides_caecimuris_GCF_001688725.2_ASM168872v2_genomic.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Ba_cd_Cavi_XX_Ba_cd_Cavi_Chlamydia_avium_10DC88_GCF_000583875.1_ASM58387v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Ba_cd_Cavi_XX_Ba_cd_Cavi_Chlamydia_avium_10DC88_GCF_000583875.1_ASM58387v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Ba_cy_Smaj_XX_Ba_cy_Smaj_Spirulina_major_PCC_6313_0GCF_001890765.1_ASM189076v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Ba_cy_Smaj_XX_Ba_cy_Smaj_Spirulina_major_PCC_6313_0GCF_001890765.1_ASM189076v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/EE_ha_Ehux_XX_EE_ha_Ehux_Filtered.Final.AA.fasta
+++ b/PTL2/Data/Raw/EE_ha_Ehux_XX_EE_ha_Ehux_Filtered.Final.AA.fasta
--- a/PTL2/Data/Raw/Ex_eu_Egym_XX_Ex_eu_Egym_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Ex_eu_Egym_XX_Ex_eu_Egym_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Op_me_Bplu_XX_Op_me_Bplu_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Op_me_Bplu_XX_Op_me_Bplu_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Pl_gr_Dsal_XX_Pl_gr_Dsal_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Pl_gr_Dsal_XX_Pl_gr_Dsal_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Pl_rh_Ccho_XX_Pl_rh_Ccho_Filtered.Final.AA.fasta
+++ b/PTL2/Data/Raw/Pl_rh_Ccho_XX_Pl_rh_Ccho_Filtered.Final.AA.fasta
--- a/PTL2/Data/Raw/Sr_ci_Ptet_XX_Sr_ci_Ptet_Paramecium_tetraurelia_strain_d4-2_genome.WGS.CDS.Renamed.Ciliate.AA.fasta
+++ b/PTL2/Data/Raw/Sr_ci_Ptet_XX_Sr_ci_Ptet_Paramecium_tetraurelia_strain_d4-2_genome.WGS.CDS.Renamed.Ciliate.AA.fasta
--- a/PTL2/Data/Raw/Sr_di_Smic_XX_Sr_di_Smic_Symbiodinium_microadriaticum.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Sr_di_Smic_XX_Sr_di_Smic_Symbiodinium_microadriaticum.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Sr_rh_As01_XX_Sr_rh_As01_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Sr_rh_As01_XX_Sr_rh_As01_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Sr_rh_Blon_XX_Sr_rh_Blon_Filtered.UC.Final.AA.ORF.fasta
+++ b/PTL2/Data/Raw/Sr_rh_Blon_XX_Sr_rh_Blon_Filtered.UC.Final.AA.ORF.fasta
--- a/PTL2/Data/Raw/Sr_st_Bhom_XX_Sr_st_Bhom_GCF_000151665.1_ASM15166v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Sr_st_Bhom_XX_Sr_st_Bhom_GCF_000151665.1_ASM15166v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Sr_st_Pinf_XX_Sr_st_Pinf_Phytophthora_infestans_GCF_000142945.1_ASM14294v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Sr_st_Pinf_XX_Sr_st_Pinf_Phytophthora_infestans_GCF_000142945.1_ASM14294v1_genomic.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Za_as_Loki_XX_Za_as_Loki_Lokiarchaeum_sp_GC14_75.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Za_as_Loki_XX_Za_as_Loki_Lokiarchaeum_sp_GC14_75.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Za_ec_Maeo_XX_Za_ec_Maeo_Methanococcus_aeolicus_Nankai-3_0GCF_000017185_1_ASM1718v1.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Za_ec_Maeo_XX_Za_ec_Maeo_Methanococcus_aeolicus_Nankai-3_0GCF_000017185_1_ASM1718v1.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Za_eh_Hvol_XX_Za_eh_Hvol_Haloferax_volcanii_DS2_0GCF_000025685_1_ASM2568v1.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Za_eh_Hvol_XX_Za_eh_Hvol_Haloferax_volcanii_DS2_0GCF_000025685_1_ASM2568v1.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Data/Raw/Za_et_Tkod_XX_Za_et_Tkod_Thermococcus_kodakarensis_KOD1_DNA_0GCF_000009965_1_ASM996v1.WGS.CDS.Renamed.Universal.AA.fasta
+++ b/PTL2/Data/Raw/Za_et_Tkod_XX_Za_et_Tkod_Thermococcus_kodakarensis_KOD1_DNA_0GCF_000009965_1_ASM996v1.WGS.CDS.Renamed.Universal.AA.fasta
--- a/PTL2/Scripts-DEV/.DS_Store
+++ b/PTL2/Scripts-DEV/.DS_Store
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/.DS_Store
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/.DS_Store
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/CheckSeqScores.py
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/CheckSeqScores.py
@ -0,0 +1,30 @@
+import os,sys
+
+
+
+with open('ScoreBySeq.tsv', 'w') as o:
+	for clade in os.listdir('GuidanceOutput'):
+		if(os.path.isfile('GuidanceOutput/' + clade + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names')):
+			for line in open('GuidanceOutput/' + clade + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
+				if('SEQUENCE_NAME' not in line):
+					o.write(line)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/CustomAlign.py
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/CustomAlign.py
@ -0,0 +1,16 @@
+import os, sys
+from Bio import SeqIO
+
+
+score_by_seq = { line.split('\t')[0] : float(line.split('\t')[1]) for line in open('ScoreBySeq.tsv') }
+
+remove3 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.3]
+remove5 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.5]
+remove7 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.7]
+
+for clade in os.listdir('GuidanceOutput'):
+	if('OG5_' in clade):
+		with open('SeqFiltered_ToAlign/Preguidance_0.7/' + clade[:12] + '.fasta', 'w') as o:
+			for rec in SeqIO.parse('GuidanceOutput/' + clade + '/Seqs.Orig.fas', 'fasta'):
+				if(rec.id not in remove7):
+					o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/NumRemovedSeqs.csv
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/NumRemovedSeqs.csv
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/COS.std
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/COS.std
@ -0,0 +1,170 @@
+--- init HoT_COS_GUIDANCE2.pl pid=6505 Sun Feb 20 00:14:47 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_0_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_0.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 20 of 125 ...
+---
+ MSA_0_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_0_cos_MFT
+Sun Feb 20 00:14:53 2022
+--- init HoT_COS_GUIDANCE2.pl pid=10893 Sun Feb 20 00:14:53 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_1_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_1.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 109 of 125 ...
+---
+ MSA_1_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_1_cos_MFT
+Sun Feb 20 00:15:00 2022
+--- init HoT_COS_GUIDANCE2.pl pid=14766 Sun Feb 20 00:15:00 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_2_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_2.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 83 of 125 ...
+---
+ MSA_2_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_2_cos_MFT
+Sun Feb 20 00:15:07 2022
+--- init HoT_COS_GUIDANCE2.pl pid=18991 Sun Feb 20 00:15:07 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_3_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_3.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 61 of 125 ...
+---
+ MSA_3_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_3_cos_MFT
+Sun Feb 20 00:15:12 2022
+--- init HoT_COS_GUIDANCE2.pl pid=23356 Sun Feb 20 00:15:12 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_4_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_4.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 77 of 125 ...
+---
+ MSA_4_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_4_cos_MFT
+Sun Feb 20 00:15:19 2022
+--- init HoT_COS_GUIDANCE2.pl pid=29089 Sun Feb 20 00:15:19 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_5_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_5.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 54 of 125 ...
+---
+ MSA_5_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_5_cos_MFT
+Sun Feb 20 00:15:25 2022
+--- init HoT_COS_GUIDANCE2.pl pid=33605 Sun Feb 20 00:15:25 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_6_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_6.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 58 of 125 ...
+---
+ MSA_6_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_6_cos_MFT
+Sun Feb 20 00:15:30 2022
+--- init HoT_COS_GUIDANCE2.pl pid=37939 Sun Feb 20 00:15:30 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_7_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_7.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 101 of 125 ...
+---
+ MSA_7_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_7_cos_MFT
+Sun Feb 20 00:15:36 2022
+--- init HoT_COS_GUIDANCE2.pl pid=43234 Sun Feb 20 00:15:36 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_8_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_8.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 73 of 125 ...
+---
+ MSA_8_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_8_cos_MFT
+Sun Feb 20 00:15:44 2022
+--- init HoT_COS_GUIDANCE2.pl pid=49264 Sun Feb 20 00:15:45 2022
+met=MFT
+infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
+seqtype=0
+outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+tgz=0
+debug=0
+basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
+output_id=MSA_9_cos_MFT
+---
+TREE_FILE:MSA.MAFFT.semphy.tree_9.rooted.GoodBranchLength
+-Making hot_H ...
+-Making hot_T ...
+-Making branch 25 of 125 ...
+---
+ MSA_9_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_9_cos_MFT
+Sun Feb 20 00:15:50 2022
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/ENDS_OK
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/ENDS_OK
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_AlternativeMSA.tar.gz
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_AlternativeMSA.tar.gz
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_BP_Dir.tar.gz
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_BP_Dir.tar.gz
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Annot
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Annot
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Features
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Features
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_col_col.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_col_col.scr
@ -0,0 +1,353 @@
+#COL_NUMBER  #COL_SCORE
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+   347  0.275000
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+   349  0.275000
+   350  0.325000
+   351  0.325000
+#END
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_msa.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_msa.scr
@ -0,0 +1,6 @@
+#REF_FILE /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.aln
+#ROWS   64  #COLUMNS    351
+#ALT_FILES -d /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/GUIDANCE2_MSA/ 
+#N_ALT     40
+#MEAN_RES_PAIR_SCORE 0.948841  #MEAN_COL_SCORE 0.009544
+#END
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair.scr
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr
@ -0,0 +1,346 @@
+#COL_NUMBER  #RES_PAIR_COLUMN_SCORE
+     1  1.000000
+     2  1.000000
+     3  1.000000
+     4  1.000000
+     7  0.924242
+     8  0.969697
+     9  0.969697
+    10  1.000000
+    11  1.000000
+    12  1.000000
+    13  1.000000
+    14  1.000000
+    15  1.000000
+    16  1.000000
+    17  1.000000
+    18  1.000000
+    19  1.000000
+    20  1.000000
+    21  1.000000
+    22  1.000000
+    23  1.000000
+    24  1.000000
+    25  1.000000
+    26  0.971795
+    27  1.000000
+    28  1.000000
+    29  1.000000
+    30  1.000000
+    31  1.000000
+    32  1.000000
+    33  1.000000
+    34  1.000000
+    35  1.000000
+    36  1.000000
+    37  1.000000
+    38  1.000000
+    39  1.000000
+    40  1.000000
+    41  1.000000
+    42  1.000000
+    43  1.000000
+    44  1.000000
+    45  1.000000
+    46  1.000000
+    47  1.000000
+    48  0.963333
+    49  0.963333
+    50  0.963333
+    51  0.963333
+    52  0.969444
+    53  0.955556
+    54  0.955556
+    55  0.955556
+    56  0.955556
+    57  0.955556
+    58  0.955556
+    59  0.955556
+    60  0.955556
+    61  0.955556
+    62  0.960000
+    63  0.960000
+    64  0.960000
+    65  0.960000
+    66  0.961905
+    67  0.961905
+    68  0.954762
+    69  0.950000
+    70  0.945238
+    71  0.942857
+    72  0.942857
+    73  0.942857
+    74  0.942857
+    75  0.942857
+    76  0.942857
+    77  0.925714
+    78  0.856190
+    79  0.936842
+    80  0.936842
+    81  0.936842
+    82  0.936842
+    83  0.936842
+    84  0.906667
+    85  0.942857
+    86  0.942857
+    87  0.942857
+    88  0.945455
+    89  0.945455
+    90  0.945455
+    91  0.945455
+    92  0.945455
+    93  0.945455
+    94  0.945455
+    95  0.945455
+    96  0.945455
+    97  0.945455
+    98  0.945455
+    99  0.945455
+   100  0.945455
+   101  0.945455
+   102  0.945455
+   103  0.945455
+   104  0.945455
+   105  0.945455
+   106  0.945455
+   107  0.945455
+   108  0.945455
+   109  0.945455
+   110  0.950000
+   111  0.919203
+   112  0.945455
+   113  0.945455
+   114  0.945455
+   115  0.945455
+   116  0.940909
+   117  1.000000
+   118  1.000000
+   119  1.000000
+   120  0.909091
+   121  0.909091
+   122  1.000000
+   123  1.000000
+   124  1.000000
+   125  1.000000
+   126  1.000000
+   127  1.000000
+   128  1.000000
+   129  1.000000
+   130  1.000000
+   131  1.000000
+   132  1.000000
+   133  1.000000
+   134  1.000000
+   135  1.000000
+   136  1.000000
+   137  1.000000
+   138  0.982684
+   139  0.982684
+   140  0.952964
+   141  0.904167
+   142  0.854654
+   143  0.837143
+   144  0.703801
+   145  1.000000
+   146  1.000000
+   147  0.984211
+   148  0.948718
+   149  0.948718
+   150  0.948718
+   151  0.948718
+   152  0.948718
+   153  0.948718
+   154  0.948718
+   156  0.948718
+   157  0.948718
+   158  0.948718
+   159  0.948718
+   160  0.948718
+   161  0.950000
+   162  0.950000
+   163  0.937317
+   164  0.938792
+   165  0.938792
+   166  0.940199
+   167  0.940199
+   168  0.940199
+   169  0.940199
+   170  0.940253
+   171  0.940253
+   172  0.940253
+   173  0.941522
+   174  0.941522
+   175  0.941522
+   176  0.941522
+   177  0.941522
+   178  0.941522
+   179  0.946102
+   180  0.946102
+   181  0.946102
+   182  0.946102
+   183  0.946102
+   184  0.946102
+   185  0.946102
+   186  0.946102
+   187  0.946102
+   188  0.902429
+   189  0.821266
+   190  0.715856
+   191  0.639517
+   192  1.000000
+   193  0.713333
+   194  0.693407
+   195  0.891209
+   196  0.938667
+   197  0.927866
+   198  0.927866
+   199  0.927866
+   200  0.927866
+   201  0.927866
+   202  0.927866
+   203  0.924165
+   204  0.923690
+   205  0.926299
+   206  0.924578
+   207  0.907477
+   208  0.898403
+   209  0.917647
+   210  0.949911
+   211  0.932707
+   212  0.932707
+   213  0.932707
+   214  0.933817
+   215  0.930395
+   216  0.930395
+   217  0.933729
+   218  0.937062
+   219  0.937062
+   220  0.937062
+   221  0.937062
+   222  0.937062
+   223  0.937062
+   224  0.937062
+   225  0.937062
+   226  0.933729
+   227  0.933729
+   228  0.933729
+   229  0.933729
+   230  0.935395
+   231  0.937062
+   232  0.937062
+   233  0.877631
+   234  0.877631
+   235  0.877631
+   236  0.877631
+   237  0.877631
+   238  0.877631
+   239  0.877631
+   240  0.877631
+   241  0.880751
+   242  0.880751
+   243  0.880751
+   244  0.880751
+   245  0.880751
+   247  0.874564
+   248  0.874564
+   249  0.874564
+   250  0.714286
+   253  0.934754
+   254  0.934754
+   255  0.938033
+   256  0.938033
+   257  0.938033
+   258  0.938033
+   259  0.941311
+   260  0.941311
+   261  0.941311
+   262  0.941311
+   263  0.938033
+   264  0.934754
+   265  0.934754
+   266  0.934754
+   267  0.934754
+   268  0.934754
+   269  0.934754
+   270  0.934754
+   271  0.975820
+   272  0.983607
+   273  0.990164
+   274  0.990164
+   275  0.990164
+   277  0.990164
+   278  0.990164
+   279  0.990164
+   280  0.990164
+   281  0.990164
+   282  0.990164
+   283  0.990164
+   284  0.990164
+   285  0.990164
+   286  0.928315
+   287  0.931388
+   288  0.961396
+   289  0.930927
+   290  0.930927
+   291  0.930927
+   292  0.993443
+   293  0.993443
+   294  0.993443
+   295  0.993443
+   296  0.993443
+   297  0.993443
+   298  0.993443
+   299  0.993443
+   300  0.993443
+   301  0.993443
+   302  0.996721
+   303  1.000000
+   304  1.000000
+   305  1.000000
+   306  1.000000
+   307  1.000000
+   308  1.000000
+   309  1.000000
+   310  1.000000
+   311  1.000000
+   312  1.000000
+   313  1.000000
+   314  1.000000
+   315  1.000000
+   316  1.000000
+   317  1.000000
+   318  0.967213
+   319  0.936013
+   320  0.936013
+   321  0.936013
+   322  0.967213
+   323  0.967213
+   324  0.967213
+   325  0.967213
+   326  0.944945
+   327  0.894737
+   328  0.967213
+   329  0.967213
+   330  0.967213
+   331  0.967213
+   332  0.967213
+   333  0.966667
+   334  0.966667
+   335  0.966667
+   336  0.966102
+   337  0.966102
+   338  0.966102
+   339  0.965517
+   340  1.000000
+   341  1.000000
+   342  1.000000
+   343  1.000000
+   344  1.000000
+   345  1.000000
+   346  1.000000
+   347  0.990323
+   348  1.000000
+   349  1.000000
+   350  0.951111
+   351  1.000000
+#END
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv
@ -0,0 +1,345 @@
+#COL_NUMBER,#RES_PAIR_COLUMN_SCORE
+1,1.000000
+2,1.000000
+3,1.000000
+4,1.000000
+7,0.924242
+8,0.969697
+9,0.969697
+10,1.000000
+11,1.000000
+12,1.000000
+13,1.000000
+14,1.000000
+15,1.000000
+16,1.000000
+17,1.000000
+18,1.000000
+19,1.000000
+20,1.000000
+21,1.000000
+22,1.000000
+23,1.000000
+24,1.000000
+25,1.000000
+26,0.971795
+27,1.000000
+28,1.000000
+29,1.000000
+30,1.000000
+31,1.000000
+32,1.000000
+33,1.000000
+34,1.000000
+35,1.000000
+36,1.000000
+37,1.000000
+38,1.000000
+39,1.000000
+40,1.000000
+41,1.000000
+42,1.000000
+43,1.000000
+44,1.000000
+45,1.000000
+46,1.000000
+47,1.000000
+48,0.963333
+49,0.963333
+50,0.963333
+51,0.963333
+52,0.969444
+53,0.955556
+54,0.955556
+55,0.955556
+56,0.955556
+57,0.955556
+58,0.955556
+59,0.955556
+60,0.955556
+61,0.955556
+62,0.960000
+63,0.960000
+64,0.960000
+65,0.960000
+66,0.961905
+67,0.961905
+68,0.954762
+69,0.950000
+70,0.945238
+71,0.942857
+72,0.942857
+73,0.942857
+74,0.942857
+75,0.942857
+76,0.942857
+77,0.925714
+78,0.856190
+79,0.936842
+80,0.936842
+81,0.936842
+82,0.936842
+83,0.936842
+84,0.906667
+85,0.942857
+86,0.942857
+87,0.942857
+88,0.945455
+89,0.945455
+90,0.945455
+91,0.945455
+92,0.945455
+93,0.945455
+94,0.945455
+95,0.945455
+96,0.945455
+97,0.945455
+98,0.945455
+99,0.945455
+100,0.945455
+101,0.945455
+102,0.945455
+103,0.945455
+104,0.945455
+105,0.945455
+106,0.945455
+107,0.945455
+108,0.945455
+109,0.945455
+110,0.950000
+111,0.919203
+112,0.945455
+113,0.945455
+114,0.945455
+115,0.945455
+116,0.940909
+117,1.000000
+118,1.000000
+119,1.000000
+120,0.909091
+121,0.909091
+122,1.000000
+123,1.000000
+124,1.000000
+125,1.000000
+126,1.000000
+127,1.000000
+128,1.000000
+129,1.000000
+130,1.000000
+131,1.000000
+132,1.000000
+133,1.000000
+134,1.000000
+135,1.000000
+136,1.000000
+137,1.000000
+138,0.982684
+139,0.982684
+140,0.952964
+141,0.904167
+142,0.854654
+143,0.837143
+144,0.703801
+145,1.000000
+146,1.000000
+147,0.984211
+148,0.948718
+149,0.948718
+150,0.948718
+151,0.948718
+152,0.948718
+153,0.948718
+154,0.948718
+156,0.948718
+157,0.948718
+158,0.948718
+159,0.948718
+160,0.948718
+161,0.950000
+162,0.950000
+163,0.937317
+164,0.938792
+165,0.938792
+166,0.940199
+167,0.940199
+168,0.940199
+169,0.940199
+170,0.940253
+171,0.940253
+172,0.940253
+173,0.941522
+174,0.941522
+175,0.941522
+176,0.941522
+177,0.941522
+178,0.941522
+179,0.946102
+180,0.946102
+181,0.946102
+182,0.946102
+183,0.946102
+184,0.946102
+185,0.946102
+186,0.946102
+187,0.946102
+188,0.902429
+189,0.821266
+190,0.715856
+191,0.639517
+192,1.000000
+193,0.713333
+194,0.693407
+195,0.891209
+196,0.938667
+197,0.927866
+198,0.927866
+199,0.927866
+200,0.927866
+201,0.927866
+202,0.927866
+203,0.924165
+204,0.923690
+205,0.926299
+206,0.924578
+207,0.907477
+208,0.898403
+209,0.917647
+210,0.949911
+211,0.932707
+212,0.932707
+213,0.932707
+214,0.933817
+215,0.930395
+216,0.930395
+217,0.933729
+218,0.937062
+219,0.937062
+220,0.937062
+221,0.937062
+222,0.937062
+223,0.937062
+224,0.937062
+225,0.937062
+226,0.933729
+227,0.933729
+228,0.933729
+229,0.933729
+230,0.935395
+231,0.937062
+232,0.937062
+233,0.877631
+234,0.877631
+235,0.877631
+236,0.877631
+237,0.877631
+238,0.877631
+239,0.877631
+240,0.877631
+241,0.880751
+242,0.880751
+243,0.880751
+244,0.880751
+245,0.880751
+247,0.874564
+248,0.874564
+249,0.874564
+250,0.714286
+253,0.934754
+254,0.934754
+255,0.938033
+256,0.938033
+257,0.938033
+258,0.938033
+259,0.941311
+260,0.941311
+261,0.941311
+262,0.941311
+263,0.938033
+264,0.934754
+265,0.934754
+266,0.934754
+267,0.934754
+268,0.934754
+269,0.934754
+270,0.934754
+271,0.975820
+272,0.983607
+273,0.990164
+274,0.990164
+275,0.990164
+277,0.990164
+278,0.990164
+279,0.990164
+280,0.990164
+281,0.990164
+282,0.990164
+283,0.990164
+284,0.990164
+285,0.990164
+286,0.928315
+287,0.931388
+288,0.961396
+289,0.930927
+290,0.930927
+291,0.930927
+292,0.993443
+293,0.993443
+294,0.993443
+295,0.993443
+296,0.993443
+297,0.993443
+298,0.993443
+299,0.993443
+300,0.993443
+301,0.993443
+302,0.996721
+303,1.000000
+304,1.000000
+305,1.000000
+306,1.000000
+307,1.000000
+308,1.000000
+309,1.000000
+310,1.000000
+311,1.000000
+312,1.000000
+313,1.000000
+314,1.000000
+315,1.000000
+316,1.000000
+317,1.000000
+318,0.967213
+319,0.936013
+320,0.936013
+321,0.936013
+322,0.967213
+323,0.967213
+324,0.967213
+325,0.967213
+326,0.944945
+327,0.894737
+328,0.967213
+329,0.967213
+330,0.967213
+331,0.967213
+332,0.967213
+333,0.966667
+334,0.966667
+335,0.966667
+336,0.966102
+337,0.966102
+338,0.966102
+339,0.965517
+340,1.000000
+341,1.000000
+342,1.000000
+343,1.000000
+344,1.000000
+345,1.000000
+346,1.000000
+347,0.990323
+348,1.000000
+349,1.000000
+350,0.951111
+351,1.000000
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr
@ -0,0 +1,66 @@
+#ROW_NUMBER #RES_PAIR_SEQUENCE_SCORE
+   1  0.972665
+   2  0.972354
+   3  0.973047
+   4  0.971883
+   5  0.972259
+   6  0.973419
+   7  0.973419
+   8  0.973315
+   9  0.973365
+  10  0.972038
+  11  0.971994
+  12  0.971994
+  13  0.967681
+  14  0.971994
+  15  0.974957
+  16  0.972037
+  17  0.972951
+  18  0.972194
+  19  0.972446
+  20  0.972026
+  21  0.972029
+  22  0.972029
+  23  0.972029
+  24  0.971957
+  25  0.971957
+  26  0.617739
+  27  0.972841
+  28  0.963693
+  29  0.972556
+  30  0.971425
+  31  0.985244
+  32  0.975988
+  33  0.970810
+  34  0.959558
+  35  0.973280
+  36  0.973217
+  37  0.973217
+  38  0.970410
+  39  0.972243
+  40  0.969683
+  41  0.523179
+  42  0.971567
+  43  0.972529
+  44  0.975371
+  45  0.975130
+  46  0.972646
+  47  0.972568
+  48  0.973136
+  49  0.974294
+  50  0.964843
+  51  0.965645
+  52  0.965526
+  53  0.964671
+  54  0.901158
+  55  0.894595
+  56  0.894595
+  57  0.834473
+  58  0.822077
+  59  0.818130
+  60  0.964955
+  61  0.378007
+  62  0.964717
+  63  0.972129
+  64  0.592674
+#END
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names
@ -0,0 +1,66 @@
+SEQUENCE_NAME	SEQUENCE_SCORE
+Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554	0.972665
+Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554	0.972354
+Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554	0.973047
+Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554	0.971883
+Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554	0.972259
+Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554	0.973419
+Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554	0.973419
+Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554	0.973315
+Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554	0.973365
+Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554	0.972038
+Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554	0.971994
+Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554	0.971994
+Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554	0.967681
+Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554	0.971994
+Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554	0.974957
+Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554	0.972037
+Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554	0.972951
+Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554	0.972194
+Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554	0.972446
+Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554	0.972026
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554	0.972029
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554	0.972029
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554	0.972029
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554	0.971957
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554	0.971957
+Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554	0.617739
+Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554	0.972841
+Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554	0.963693
+Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554	0.972556
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554	0.971425
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554	0.985244
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554	0.975988
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554	0.970810
+Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554	0.959558
+Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554	0.973280
+Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554	0.973217
+Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554	0.973217
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554	0.970410
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554	0.972243
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554	0.969683
+Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554	0.523179
+Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554	0.971567
+Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554	0.972529
+Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554	0.975371
+Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554	0.975130
+Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554	0.972646
+Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554	0.972568
+Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554	0.973136
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554	0.974294
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554	0.964843
+Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554	0.965645
+Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554	0.965526
+Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554	0.964671
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554	0.901158
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554	0.894595
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554	0.894595
+Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554	0.834473
+Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554	0.822077
+Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554	0.818130
+Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554	0.964955
+Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554	0.378007
+Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554	0.964717
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554	0.972129
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554	0.592674
+#END
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq_pair.scr
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq_pair.scr
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance_res_pair_res.html
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Guidance_res_pair_res.html
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col
@ -0,0 +1,128 @@
+>seq0000
+-------------------------------------------------------------------------------------------------------------ISFDASVFKWGELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
+>seq0001
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
+>seq0002
+-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>seq0003
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
+>seq0004
+-------------------------------------------------------------------------------------------------------------ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>seq0005
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>seq0006
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>seq0007
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
+>seq0008
+PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
+>seq0009
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>seq0010
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>seq0011
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>seq0012
+-----------------------------------------------------------------------------------------------------------------------RS----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
+>seq0013
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>seq0014
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
+>seq0015
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
+>seq0016
+PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLLSWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
+>seq0017
+-----------------------------------------------------------------FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
+>seq0018
+---------------------------------------------------------------------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
+>seq0019
+--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
+>seq0020
+---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0021
+---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0022
+---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0023
+-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0024
+-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0025
+PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>seq0026
+PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLLSWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
+>seq0027
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------ITMNFIIAGKDTTAQLLSWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
+>seq0028
+--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLLSWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
+>seq0029
+----------------------------------------------------------------------------------------------------------------------------------------------------------------LRDVAMNFIIAGRDTTAQLLSWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>seq0030
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>seq0031
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
+>seq0032
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
+>seq0033
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------RVRAAQLLSWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
+>seq0034
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
+>seq0035
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>seq0036
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>seq0037
+--------------------------------------------------------------------------------------------------------------------------------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
+>seq0038
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
+>seq0039
+----------------------------------------------------------------------------------------------------------------------------------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTLSWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
+>seq0040
+PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS-------------------------------------------------------------------------------------------------------------------------QAPEELEFTSFDK-ICK------------------------------------RF-FDP---------------------------IKM------------------------------
+>seq0041
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
+>seq0042
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>seq0043
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>seq0044
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
+>seq0045
+--------------------------------------------------------------------------------------------------------------------------------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
+>seq0046
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------INFIIAGKDTTAQMLSWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
+>seq0047
+PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
+>seq0048
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>seq0049
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMLSWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>seq0050
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
+>seq0051
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
+>seq0052
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MLSWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
+>seq0053
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
+>seq0054
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
+>seq0055
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
+>seq0056
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
+>seq0057
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
+>seq0058
+------------------------------------------------------------------------------------------------------------------------------------------------------------------DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
+>seq0059
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
+>seq0060
+------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE-------------------------------------------------------------------------------------------------------------------------QAPHDTRFEAFDG-GCD------------------------------------RFIARP--------------------------FLETLKHAKRFCSIRERIESGE------------
+>seq0061
+-------------------------------------------------------------------------------------------------------------------------------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQAKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME--------------------------------------
+>seq0062
+--------------------------------------------------------------------------------------------------------------------------------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRFAFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
+>seq0063
+---------------------------------------------------------------------------------------------------------------------------------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col.With_Names
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col.With_Names
@ -0,0 +1,128 @@
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
+-------------------------------------------------------------------------------------------------------------ISFDASVFKWGELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
+>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
+-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
+>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
+-------------------------------------------------------------------------------------------------------------ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
+>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
+PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
+>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
+-----------------------------------------------------------------------------------------------------------------------RS----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
+>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
+>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
+PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLLSWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
+>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
+-----------------------------------------------------------------FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
+---------------------------------------------------------------------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
+>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
+--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
+---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
+---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
+---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
+-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
+-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
+PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
+PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLLSWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------ITMNFIIAGKDTTAQLLSWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
+--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLLSWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------LRDVAMNFIIAGRDTTAQLLSWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------RVRAAQLLSWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
+>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTLSWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
+>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
+PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS-------------------------------------------------------------------------------------------------------------------------QAPEELEFTSFDK-ICK------------------------------------RF-FDP---------------------------IKM------------------------------
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
+>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------INFIIAGKDTTAQMLSWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
+>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
+PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMLSWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
+>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MLSWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
+-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
+>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
+------------------------------------------------------------------------------------------------------------------------------------------------------------------DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
+----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
+>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
+------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE-------------------------------------------------------------------------------------------------------------------------QAPHDTRFEAFDG-GCD------------------------------------RFIARP--------------------------FLETLKHAKRFCSIRERIESGE------------
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
+-------------------------------------------------------------------------------------------------------------------------------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQAKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME--------------------------------------
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
+--------------------------------------------------------------------------------------------------------------------------------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRFAFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
+---------------------------------------------------------------------------------------------------------------------------------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.aln
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.aln
@ -0,0 +1,448 @@
+>seq0000
+------------------------------------------------------------
+-------------------------------------------------ISFDASVFKWG
+ELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLL
+SWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRF
+ATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIP
+PRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
+>seq0001
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLL
+SWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRF
+ATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVP
+PRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
+>seq0002
+-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRD
+YMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVR
+TLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
+SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
+AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
+PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>seq0003
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------LL
+SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
+AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
+PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
+>seq0004
+------------------------------------------------------------
+-------------------------------------------------ISFDDGQTRVR
+TLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
+SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
+AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
+PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>seq0005
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
+YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
+TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
+SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
+AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>seq0006
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
+YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
+TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
+SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
+AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>seq0007
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
+YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
+TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
+SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
+AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
+>seq0008
+PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRD
+YMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKAR
+TLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLL
+SWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRY
+AKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIP
+PRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
+>seq0009
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------LM
+SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
+AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
+PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>seq0010
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLM
+SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
+AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
+PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>seq0011
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
+SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
+AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>seq0012
+------------------------------------------------------------
+-----------------------------------------------------------R
+S----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
+SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
+AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
+>seq0013
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
+SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
+AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>seq0014
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRY
+AKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIP
+PRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
+>seq0015
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLL
+SWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRY
+AKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
+>seq0016
+PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRD
+YMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLK
+SLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLL
+SWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRY
+AKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIP
+PRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
+>seq0017
+------------------------------------------------------------
+-----FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWR
+TLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLL
+SWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRY
+AKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
+>seq0018
+------------------------------------------------------------
+---------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLR
+ELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLL
+SWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRF
+AKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIP
+PRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
+>seq0019
+--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRD
+FMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFK
+ELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLC
+SWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRF
+ALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIP
+PRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
+>seq0020
+---------------------------------------------------MFTVRALRD
+YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0021
+---------------------------------------------------MFTVRALRD
+YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0022
+---------------------------------------------------MFTVRALRD
+YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0023
+------------------------------------------------------------
+-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0024
+------------------------------------------------------------
+-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>seq0025
+PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRD
+YMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ----
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------
+>seq0026
+PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLRE
+YMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWR
+ELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLL
+SWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRY
+AKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIP
+PRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
+>seq0027
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------ITMNFIIAGKDTTAQLL
+SWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRF
+AKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIP
+PRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
+>seq0028
+--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRD
+YMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFK
+ELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLL
+SWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVRE
+AKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIP
+PRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
+>seq0029
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------LRDVAMNFIIAGRDTTAQLL
+SWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRF
+AKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
+PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>seq0030
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
+PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>seq0031
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------IKLNYLENSFLETLRLRPSVPHLVRK
+AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
+>seq0032
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRK
+AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
+>seq0033
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------RVRAAQLL
+SWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQ
+ANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
+>seq0034
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQ
+ANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
+>seq0035
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
+YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
+ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
+SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
+AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
+PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>seq0036
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
+YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
+ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
+SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
+AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
+PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>seq0037
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
+SWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRF
+ATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIA
+PRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
+>seq0038
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
+SWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRF
+ATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIA
+PRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
+>seq0039
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTL
+SWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRY
+ATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVA
+PRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
+>seq0040
+PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRD
+YMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS---------
+------------------------------------------------------------
+----------------------------------------------------QAPEELEF
+TSFDK-ICK------------------------------------RF-FDP---------
+------------------IKM------------------------------
+>seq0041
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
+SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
+AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
+>seq0042
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
+SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
+AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>seq0043
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------KVKCSFIECCLKESLRLYPSVPHLVRT
+AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>seq0044
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRT
+AVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
+>seq0045
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQML
+SWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRT
+PVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIA
+PRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
+>seq0046
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------INFIIAGKDTTAQML
+SWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRT
+AVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVA
+PRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
+>seq0047
+PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRD
+YMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKK
+EMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQML
+SWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARA
+AVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIP
+PRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
+>seq0048
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
+AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
+PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>seq0049
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------------IAGRDTTSQML
+SWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
+AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
+PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>seq0050
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQML
+SWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRT
+AIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLK
+PRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
+>seq0051
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHML
+SWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRT
+AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQ
+PRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
+>seq0052
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------ML
+SWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRT
+AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQ
+PRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
+>seq0053
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------VECKYIECCLKETLRLYPSVPHFSRE
+MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIA
+PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
+>seq0054
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSRE
+MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIA
+PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
+>seq0055
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSRE
+MVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNIS
+PRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
+>seq0056
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------------IAGRDTTSQMI
+SWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQ
+MVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIA
+PRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
+>seq0057
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQML
+SWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVRE
+MVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIA
+PRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
+>seq0058
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------DITMNFIIAGRDTTSQML
+SWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVRE
+MVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNIL
+PRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
+>seq0059
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------LL
+SWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
+AVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIA
+PRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
+>seq0060
+------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKH
+YMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE---------
+------------------------------------------------------------
+----------------------------------------------------QAPHDTRF
+EAFDG-GCD------------------------------------RFIARP---------
+-----------------FLETLKHAKRFCSIRERIESGE------------
+>seq0061
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENI
+SWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQ
+AKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIA
+PRMCLGKHVAMME--------------------------------------
+>seq0062
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETL
+TWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRF
+AFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIG
+QRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
+>seq0063
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNL
+CWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRV
+AVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIG
+QRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.aln.With_Names
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.aln.With_Names
@ -0,0 +1,448 @@
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
+------------------------------------------------------------
+-------------------------------------------------ISFDASVFKWG
+ELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLL
+SWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRF
+ATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIP
+PRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLL
+SWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRF
+ATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVP
+PRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
+>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
+-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRD
+YMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVR
+TLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
+SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
+AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
+PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------LL
+SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
+AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
+PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
+>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
+------------------------------------------------------------
+-------------------------------------------------ISFDDGQTRVR
+TLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
+SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
+AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
+PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
+>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
+YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
+TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
+SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
+AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
+YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
+TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
+SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
+AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
+>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
+PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
+YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
+TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
+SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
+AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
+>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
+PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRD
+YMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKAR
+TLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLL
+SWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRY
+AKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIP
+PRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
+>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------LM
+SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
+AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
+PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLM
+SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
+AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
+PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
+SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
+AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
+------------------------------------------------------------
+-----------------------------------------------------------R
+S----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
+SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
+AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
+SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
+AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRY
+AKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIP
+PRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
+>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLL
+SWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRY
+AKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
+>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
+PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRD
+YMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLK
+SLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLL
+SWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRY
+AKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIP
+PRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
+>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
+------------------------------------------------------------
+-----FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWR
+TLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLL
+SWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRY
+AKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLP
+PRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
+------------------------------------------------------------
+---------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLR
+ELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLL
+SWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRF
+AKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIP
+PRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
+>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
+--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRD
+FMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFK
+ELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLC
+SWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRF
+ALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIP
+PRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
+---------------------------------------------------MFTVRALRD
+YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
+---------------------------------------------------MFTVRALRD
+YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
+---------------------------------------------------MFTVRALRD
+YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
+------------------------------------------------------------
+-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
+------------------------------------------------------------
+-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
+ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
+SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
+AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
+PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
+PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRD
+YMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ----
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------------
+>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
+PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLRE
+YMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWR
+ELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLL
+SWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRY
+AKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIP
+PRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------ITMNFIIAGKDTTAQLL
+SWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRF
+AKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIP
+PRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
+--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRD
+YMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFK
+ELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLL
+SWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVRE
+AKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIP
+PRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------LRDVAMNFIIAGRDTTAQLL
+SWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRF
+AKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
+PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
+PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------IKLNYLENSFLETLRLRPSVPHLVRK
+AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRK
+AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------RVRAAQLL
+SWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQ
+ANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQ
+ANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIK
+PRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
+>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
+YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
+ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
+SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
+AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
+PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
+PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
+YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
+ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
+SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
+AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
+PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
+SWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRF
+ATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIA
+PRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
+SWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRF
+ATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIA
+PRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTL
+SWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRY
+ATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVA
+PRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
+>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
+PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRD
+YMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS---------
+------------------------------------------------------------
+----------------------------------------------------QAPEELEF
+TSFDK-ICK------------------------------------RF-FDP---------
+------------------IKM------------------------------
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
+SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
+AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
+SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
+AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------KVKCSFIECCLKESLRLYPSVPHLVRT
+AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRT
+AVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIA
+PRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
+>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQML
+SWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRT
+PVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIA
+PRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------------------------INFIIAGKDTTAQML
+SWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRT
+AVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVA
+PRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
+>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
+PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRD
+YMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKK
+EMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQML
+SWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARA
+AVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIP
+PRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
+AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
+PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------------IAGRDTTSQML
+SWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
+AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
+PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
+>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQML
+SWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRT
+AIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLK
+PRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHML
+SWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRT
+AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQ
+PRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
+>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------ML
+SWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRT
+AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQ
+PRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------VECKYIECCLKETLRLYPSVPHFSRE
+MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIA
+PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSRE
+MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIA
+PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSRE
+MVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNIS
+PRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------------------------IAGRDTTSQMI
+SWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQ
+MVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIA
+PRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQML
+SWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVRE
+MVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIA
+PRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
+>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------DITMNFIIAGRDTTSQML
+SWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVRE
+MVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNIL
+PRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------------LL
+SWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
+AVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIA
+PRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
+>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
+------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKH
+YMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE---------
+------------------------------------------------------------
+----------------------------------------------------QAPHDTRF
+EAFDG-GCD------------------------------------RFIARP---------
+-----------------FLETLKHAKRFCSIRERIESGE------------
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENI
+SWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQ
+AKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIA
+PRMCLGKHVAMME--------------------------------------
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETL
+TWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRF
+AFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIG
+QRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNL
+CWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRV
+AVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIG
+QRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.msa_set_score.std
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.msa_set_score.std
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.semphy.tree
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/MSA.MAFFT.semphy.tree
@ -0,0 +1 @@
+((seq0017:0.159520,((((seq0029:0.000335,seq0030:0.000001):0.298687,((seq0026:0.118374,((seq0022:0.000001,(seq0021:0.000001,(seq0020:0.000001,(seq0023:0.000001,seq0024:0.000001):0.003307):0.001691):0.000865):0.194370,(seq0019:0.213074,(seq0047:0.000001,(seq0040:0.218288,seq0060:0.741067):0.558436):0.264600):0.089062):0.026603):0.078072,(((seq0059:0.416185,(((seq0051:0.002343,seq0052:0.051365):0.156768,(seq0050:0.102723,(seq0048:0.000001,seq0049:0.000606):0.156109):0.026679):0.088477,(seq0046:0.251155,(((seq0055:0.122540,(seq0053:0.000001,seq0054:0.050064):0.060836):0.112993,(seq0058:0.094203,(seq0056:0.146811,seq0057:0.074128):0.032205):0.099845):0.238408,(seq0045:0.176854,(seq0044:0.062128,(seq0041:0.000001,(seq0042:0.014202,seq0043:0.000001):0.007922):0.069848):0.072547):0.053735):0.020337):0.040887):0.078664):0.063075,((seq0039:0.164075,(seq0037:0.088700,seq0038:0.060206):0.105530):0.093641,((seq0000:0.095561,seq0001:0.071802):0.371565,(seq0061:0.262548,(seq0062:0.274390,(seq0025:0.000001,seq0063:0.456008):0.072702):0.040402):0.114369):0.042115):0.053357):0.040190,(seq0027:0.279481,seq0028:0.236863):0.026728):0.009003):0.005029):0.027732,(seq0018:0.176464,((seq0035:0.000001,seq0036:0.000001):0.279842,((seq0033:0.064803,seq0034:0.034665):0.126784,(seq0031:0.000001,seq0032:0.021257):0.110018):0.058727):0.055398):0.008537):0.026864,(seq0015:0.079754,seq0016:0.205938):0.020846):0.015120):0.020439,((seq0009:0.022972,seq0010:0.000001):0.164226,(seq0014:0.189401,(seq0011:0.000001,(seq0012:0.012592,seq0013:0.000001):0.003812):0.062063):0.019146):0.014995,(seq0008:0.161694,((seq0007:0.000001,(seq0005:0.000001,seq0006:0.000001):0.002884):0.117868,(seq0002:0.000001,(seq0003:0.002943,seq0004:0.003582):0.007856):0.097737):0.007560):0.006500);
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/SampledOPVals.log
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/SampledOPVals.log
@ -0,0 +1,10 @@
+2.000817428956
+2.58462865668747
+1.49936059497511
+1.23331485380722
+2.15783221114012
+2.90590667209469
+2.63676633992571
+2.80645936921989
+1.84405518368005
+2.13819830457351
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Codes
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Codes
@ -0,0 +1,64 @@
+Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554	seq0000
+Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554	seq0001
+Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554	seq0002
+Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554	seq0003
+Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554	seq0004
+Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554	seq0005
+Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554	seq0006
+Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554	seq0007
+Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554	seq0008
+Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554	seq0009
+Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554	seq0010
+Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554	seq0011
+Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554	seq0012
+Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554	seq0013
+Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554	seq0014
+Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554	seq0015
+Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554	seq0016
+Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554	seq0017
+Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554	seq0018
+Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554	seq0019
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554	seq0020
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554	seq0021
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554	seq0022
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554	seq0023
+Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554	seq0024
+Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554	seq0025
+Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554	seq0026
+Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554	seq0027
+Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554	seq0028
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554	seq0029
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554	seq0030
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554	seq0031
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554	seq0032
+Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554	seq0033
+Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554	seq0034
+Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554	seq0035
+Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554	seq0036
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554	seq0037
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554	seq0038
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554	seq0039
+Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554	seq0040
+Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554	seq0041
+Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554	seq0042
+Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554	seq0043
+Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554	seq0044
+Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554	seq0045
+Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554	seq0046
+Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554	seq0047
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554	seq0048
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554	seq0049
+Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554	seq0050
+Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554	seq0051
+Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554	seq0052
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554	seq0053
+Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554	seq0054
+Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554	seq0055
+Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554	seq0056
+Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554	seq0057
+Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554	seq0058
+Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554	seq0059
+Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554	seq0060
+Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554	seq0061
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554	seq0062
+Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554	seq0063
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas
@ -0,0 +1,192 @@
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
+ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
+
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
+YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFINFIDRSTK
+
+>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
+IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
+LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
+
+>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
+ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+
+>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
+
+>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
+PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPETIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
+
+>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
+LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+
+>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
+YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
+
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
+RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLDALPSVMKNGFKVRLVPRCK
+
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
+
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
+MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAMGRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEALPTVMKNGFKVKLIPRCK
+
+>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
+YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIWNDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRNGFKVKLIPRDSK
+
+>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
+PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYELSNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHIIRKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
+
+>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
+FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIRKGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
+
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
+NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSLFLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKLVPR
+
+>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
+KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKDLLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGFYARLQPRAQQQQ
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
+PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
+
+>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
+PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLLTNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIRKGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYRIVAIPSVMKNGFKVRLELR
+
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
+ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
+
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
+LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCDLLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFKVKLVPRDTQ
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
+LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
+YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
+IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQT
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
+NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQTQF
+
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
+RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
+
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
+SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYAMGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFEPIKSVMKNGFKVKVVPIE
+
+>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
+KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISHLWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPMKNGFKVTLHNIETD
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
+YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGFKVTLECRN
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
+IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLWPDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRYGFKVKLHPRL
+
+>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
+PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICKRFFDPIKM
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
+
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
+
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
+KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
+
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
+EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWVWEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK
+
+>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
+FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLWDDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR
+
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
+INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
+
+>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
+PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYYTIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
+IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
+IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+
+>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
+YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKYIWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE
+
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
+YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK
+
+>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
+MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
+VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
+IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
+IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGDEIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE
+
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
+IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
+
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
+YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGKLPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK
+
+>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
+DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
+
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
+LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
+
+>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
+QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARPFLETLKHAKRFCSIRERIESGE
+
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
+ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEINTLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAPWIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
+YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTYESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNGFQVHLQPLHPTQN
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
+DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLPMRIIPLSSSV
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED
@ -0,0 +1,128 @@
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
+ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
+YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFINFIDRSTK
+>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
+IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
+LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
+>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
+ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
+>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
+PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPETIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
+>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
+LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
+YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
+RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLDALPSVMKNGFKVRLVPRCK
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
+MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAMGRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEALPTVMKNGFKVKLIPRCK
+>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
+YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIWNDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRNGFKVKLIPRDSK
+>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
+PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYELSNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHIIRKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
+>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
+FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIRKGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
+NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSLFLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKLVPR
+>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
+KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKDLLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGFYARLQPRAQQQQ
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
+PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
+>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
+PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLLTNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIRKGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYRIVAIPSVMKNGFKVRLELR
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
+ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
+LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCDLLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFKVKLVPRDTQ
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
+LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
+YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
+IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQT
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
+NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQTQF
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
+RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
+SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYAMGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFEPIKSVMKNGFKVKVVPIE
+>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
+KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISHLWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPMKNGFKVTLHNIETD
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
+YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGFKVTLECRN
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
+IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLWPDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRYGFKVKLHPRL
+>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
+PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICKRFFDPIKM
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
+KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
+EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWVWEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK
+>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
+FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLWDDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
+INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
+>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
+PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYYTIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
+IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
+IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
+YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKYIWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
+YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK
+>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
+MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
+VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
+IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
+IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGDEIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
+IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
+YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGKLPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK
+>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
+DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
+LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
+>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
+QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARPFLETLKHAKRFCSIRERIESGE
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
+ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEINTLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAPWIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
+YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTYESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNGFQVHLQPLHPTQN
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
+DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLPMRIIPLSSSV
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.MSA.MAFFT.Removed_Col
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.MSA.MAFFT.Removed_Col
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq
@ -0,0 +1,20 @@
+>seq0025
+PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYM
+FEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
+
+>seq0040
+PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYM
+FKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICK
+RFFDPIKM
+
+>seq0060
+QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFET
+CSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARP
+FLETLKHAKRFCSIRERIESGE
+
+>seq0063
+DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKT
+LDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENP
+LQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLP
+MRIIPLSSSV
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq.With_Names
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq.With_Names
@ -0,0 +1,20 @@
+>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
+PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYM
+FEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
+
+>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
+PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYM
+FKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICK
+RFFDPIKM
+
+>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
+QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFET
+CSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARP
+FLETLKHAKRFCSIRERIESGE
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
+DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKT
+LDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENP
+LQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLP
+MRIIPLSSSV
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq
@ -0,0 +1,366 @@
+>seq0000
+ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDT
+TAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATR
+DIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKH
+VAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
+
+>seq0001
+YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSV
+KMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENAL
+QFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFI
+NFIDRSTK
+
+>seq0002
+IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKC
+ELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTII
+QKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMRE
+IEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAM
+GRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEA
+VPSVMKYGFKVKLIPR
+
+>seq0003
+LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAK
+VDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGK
+HVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
+
+>seq0004
+ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAG
+RDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPH
+LIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPP
+RLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+
+>seq0005
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>seq0006
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>seq0007
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
+
+>seq0008
+PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYM
+FQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTL
+KAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSY
+AMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPE
+TIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEA
+KIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
+
+>seq0009
+LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAK
+VDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGK
+HVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+
+>seq0010
+YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGD
+YNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIW
+KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKN
+GLKVRLIPRGK
+
+>seq0011
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
+YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
+KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
+GFKVRLVPRCK
+
+>seq0012
+RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIM
+QEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTY
+AMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKL
+DALPSVMKNGFKVRLVPRCK
+
+>seq0013
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
+YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
+KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
+GFKVRLVPRCK
+
+>seq0014
+MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAM
+GRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEA
+LPTVMKNGFKVKLIPRCK
+
+>seq0015
+YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGD
+YNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIW
+NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRN
+GFKVKLIPRDSK
+
+>seq0016
+PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYM
+FNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSL
+KKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYEL
+SNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHII
+RKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKI
+AIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
+
+>seq0017
+FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKH
+LKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVT
+ENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIR
+KGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIA
+IIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
+
+>seq0018
+NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSL
+FLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKC
+QYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKF
+DPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKL
+VPR
+
+>seq0019
+KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDL
+YNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKD
+LLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQ
+MVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPK
+PLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGF
+YARLQPRAQQQQ
+
+>seq0020
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0021
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0022
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0023
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
+LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
+FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
+PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
+ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0024
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
+LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
+FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
+PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
+ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0026
+PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYM
+FEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWREL
+HIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLL
+TNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIR
+KGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIV
+IIKLLRKYRIVAIPSVMKNGFKVRLELR
+
+>seq0027
+ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLL
+ETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQF
+LPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
+
+>seq0028
+LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDL
+YDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCD
+LLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGK
+IKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKP
+EEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFK
+VKLVPRDTQ
+
+>seq0029
+LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFE
+TLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSP
+SKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>seq0030
+YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLE
+AKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>seq0031
+IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDA
+LKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFR
+VKLIKRQT
+
+>seq0032
+NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKD
+DTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIV
+KLFKKYKFIPIESLMKNGFRVKLIKRQTQF
+
+>seq0033
+RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHL
+VRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPR
+LCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
+
+>seq0034
+SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYA
+MGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFE
+PIKSVMKNGFKVKVVPIE
+
+>seq0035
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
+FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
+KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
+ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
+IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
+IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>seq0036
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
+FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
+KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
+ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
+IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
+IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>seq0037
+KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVI
+GTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISH
+LWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPM
+KNGFKVTLHNIETD
+
+>seq0038
+YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYH
+LIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNN
+PHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGF
+KVTLECRN
+
+>seq0039
+IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGT
+YENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLW
+PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRY
+GFKVKLHPRL
+
+>seq0041
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
+YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
+KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
+AG
+
+>seq0042
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
+YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
+KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
+AGFQAHLQK
+
+>seq0043
+KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKD
+PLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
+FQAHLQK
+
+>seq0044
+EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWV
+WEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPM
+GAGFQAHLQK
+
+>seq0045
+FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGD
+YEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLW
+DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPME
+TGFKAHLNVR
+
+>seq0046
+INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLR
+LYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRF
+PAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
+
+>seq0047
+PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYM
+FDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEM
+RSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTY
+HLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYY
+TIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEG
+KIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
+
+>seq0048
+IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSM
+GRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQ
+AFQSAMKNGLKVVLK
+
+>seq0049
+IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRL
+YPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYP
+AFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+
+>seq0050
+YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIF
+GTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKY
+IWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSA
+MKNGWKVTLE
+
+>seq0051
+YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNI
+FGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSK
+YIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPS
+AMKNGWKLDLK
+
+>seq0052
+MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLR
+TAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLC
+LGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
+
+>seq0053
+VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWEN
+ADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
+
+>seq0054
+IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGD
+EIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVA
+MFTNFKSFQAVPAAMDGGFKIHIH
+
+>seq0055
+IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGD
+EIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIA
+MFSQFKSFRTVPAAMDGGFNIYVE
+
+>seq0056
+IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLR
+LYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEI
+WPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
+
+>seq0057
+YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVD
+VFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGK
+LPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTV
+PAPFRNGFNIYLK
+
+>seq0058
+DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEA
+CLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPER
+FIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
+
+>seq0059
+LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
+AVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAP
+RICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
+
+>seq0061
+ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEIN
+TLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAP
+WIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
+
+>seq0062
+YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTY
+ESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWE
+NPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNG
+FQVHLQPLHPTQN
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names
@ -0,0 +1,366 @@
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
+ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDT
+TAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATR
+DIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKH
+VAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
+
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
+YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSV
+KMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENAL
+QFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFI
+NFIDRSTK
+
+>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
+IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKC
+ELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTII
+QKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMRE
+IEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAM
+GRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEA
+VPSVMKYGFKVKLIPR
+
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
+LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAK
+VDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGK
+HVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
+
+>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
+ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAG
+RDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPH
+LIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPP
+RLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+
+>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
+
+>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
+PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYM
+FQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTL
+KAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSY
+AMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPE
+TIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEA
+KIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
+
+>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
+LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAK
+VDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGK
+HVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+
+>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
+YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGD
+YNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIW
+KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKN
+GLKVRLIPRGK
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
+YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
+KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
+GFKVRLVPRCK
+
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
+RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIM
+QEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTY
+AMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKL
+DALPSVMKNGFKVRLVPRCK
+
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
+YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
+KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
+GFKVRLVPRCK
+
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
+MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAM
+GRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEA
+LPTVMKNGFKVKLIPRCK
+
+>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
+YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGD
+YNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIW
+NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRN
+GFKVKLIPRDSK
+
+>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
+PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYM
+FNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSL
+KKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYEL
+SNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHII
+RKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKI
+AIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
+
+>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
+FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKH
+LKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVT
+ENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIR
+KGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIA
+IIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
+
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
+NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSL
+FLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKC
+QYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKF
+DPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKL
+VPR
+
+>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
+KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDL
+YNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKD
+LLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQ
+MVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPK
+PLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGF
+YARLQPRAQQQQ
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
+LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
+FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
+PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
+ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
+LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
+FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
+PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
+ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
+PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYM
+FEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWREL
+HIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLL
+TNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIR
+KGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIV
+IIKLLRKYRIVAIPSVMKNGFKVRLELR
+
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
+ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLL
+ETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQF
+LPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
+
+>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
+LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDL
+YDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCD
+LLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGK
+IKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKP
+EEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFK
+VKLVPRDTQ
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
+LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFE
+TLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSP
+SKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
+YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLE
+AKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
+IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDA
+LKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFR
+VKLIKRQT
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
+NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKD
+DTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIV
+KLFKKYKFIPIESLMKNGFRVKLIKRQTQF
+
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
+RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHL
+VRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPR
+LCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
+
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
+SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYA
+MGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFE
+PIKSVMKNGFKVKVVPIE
+
+>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
+FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
+KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
+ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
+IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
+IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
+FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
+KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
+ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
+IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
+IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
+KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVI
+GTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISH
+LWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPM
+KNGFKVTLHNIETD
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
+YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYH
+LIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNN
+PHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGF
+KVTLECRN
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
+IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGT
+YENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLW
+PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRY
+GFKVKLHPRL
+
+>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
+YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
+KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
+AG
+
+>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
+YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
+KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
+AGFQAHLQK
+
+>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
+KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKD
+PLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
+FQAHLQK
+
+>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
+EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWV
+WEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPM
+GAGFQAHLQK
+
+>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
+FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGD
+YEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLW
+DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPME
+TGFKAHLNVR
+
+>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
+INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLR
+LYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRF
+PAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
+
+>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
+PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYM
+FDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEM
+RSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTY
+HLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYY
+TIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEG
+KIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
+IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSM
+GRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQ
+AFQSAMKNGLKVVLK
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
+IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRL
+YPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYP
+AFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+
+>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
+YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIF
+GTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKY
+IWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSA
+MKNGWKVTLE
+
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
+YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNI
+FGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSK
+YIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPS
+AMKNGWKLDLK
+
+>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
+MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLR
+TAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLC
+LGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
+VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWEN
+ADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
+
+>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
+IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGD
+EIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVA
+MFTNFKSFQAVPAAMDGGFKIHIH
+
+>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
+IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGD
+EIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIA
+MFSQFKSFRTVPAAMDGGFNIYVE
+
+>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
+IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLR
+LYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEI
+WPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
+
+>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
+YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVD
+VFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGK
+LPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTV
+PAPFRNGFNIYLK
+
+>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
+DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEA
+CLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPER
+FIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
+
+>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
+LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
+AVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAP
+RICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
+
+>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
+ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEIN
+TLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAP
+WIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
+
+>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
+YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTY
+ESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWE
+NPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNG
+FQVHLQPLHPTQN
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.numberd.fas
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/Seqs.numberd.fas
@ -0,0 +1,386 @@
+>seq0000
+ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDT
+TAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATR
+DIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKH
+VAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
+
+>seq0001
+YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSV
+KMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENAL
+QFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFI
+NFIDRSTK
+
+>seq0002
+IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKC
+ELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTII
+QKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMRE
+IEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAM
+GRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEA
+VPSVMKYGFKVKLIPR
+
+>seq0003
+LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAK
+VDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGK
+HVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
+
+>seq0004
+ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAG
+RDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPH
+LIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPP
+RLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
+
+>seq0005
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>seq0006
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
+
+>seq0007
+PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
+FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
+KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
+LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
+IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
+KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
+
+>seq0008
+PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYM
+FQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTL
+KAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSY
+AMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPE
+TIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEA
+KIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
+
+>seq0009
+LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAK
+VDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGK
+HVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
+
+>seq0010
+YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGD
+YNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIW
+KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKN
+GLKVRLIPRGK
+
+>seq0011
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
+YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
+KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
+GFKVRLVPRCK
+
+>seq0012
+RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIM
+QEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTY
+AMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKL
+DALPSVMKNGFKVRLVPRCK
+
+>seq0013
+YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
+YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
+KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
+GFKVRLVPRCK
+
+>seq0014
+MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAM
+GRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEA
+LPTVMKNGFKVKLIPRCK
+
+>seq0015
+YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGD
+YNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIW
+NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRN
+GFKVKLIPRDSK
+
+>seq0016
+PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYM
+FNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSL
+KKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYEL
+SNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHII
+RKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKI
+AIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
+
+>seq0017
+FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKH
+LKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVT
+ENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIR
+KGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIA
+IIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
+
+>seq0018
+NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSL
+FLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKC
+QYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKF
+DPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKL
+VPR
+
+>seq0019
+KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDL
+YNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKD
+LLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQ
+MVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPK
+PLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGF
+YARLQPRAQQQQ
+
+>seq0020
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0021
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0022
+MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
+FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
+KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
+VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
+VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0023
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
+LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
+FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
+PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
+ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0024
+MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
+LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
+FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
+PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
+ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
+
+>seq0025
+PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYM
+FEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
+
+>seq0026
+PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYM
+FEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWREL
+HIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLL
+TNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIR
+KGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIV
+IIKLLRKYRIVAIPSVMKNGFKVRLELR
+
+>seq0027
+ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLL
+ETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQF
+LPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
+
+>seq0028
+LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDL
+YDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCD
+LLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGK
+IKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKP
+EEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFK
+VKLVPRDTQ
+
+>seq0029
+LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFE
+TLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSP
+SKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>seq0030
+YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLE
+AKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
+
+>seq0031
+IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDA
+LKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFR
+VKLIKRQT
+
+>seq0032
+NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKD
+DTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIV
+KLFKKYKFIPIESLMKNGFRVKLIKRQTQF
+
+>seq0033
+RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHL
+VRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPR
+LCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
+
+>seq0034
+SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYA
+MGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFE
+PIKSVMKNGFKVKVVPIE
+
+>seq0035
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
+FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
+KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
+ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
+IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
+IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>seq0036
+PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
+FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
+KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
+ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
+IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
+IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
+
+>seq0037
+KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVI
+GTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISH
+LWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPM
+KNGFKVTLHNIETD
+
+>seq0038
+YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYH
+LIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNN
+PHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGF
+KVTLECRN
+
+>seq0039
+IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGT
+YENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLW
+PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRY
+GFKVKLHPRL
+
+>seq0040
+PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYM
+FKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICK
+RFFDPIKM
+
+>seq0041
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
+YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
+KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
+AG
+
+>seq0042
+YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
+YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
+KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
+AGFQAHLQK
+
+>seq0043
+KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKD
+PLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
+FQAHLQK
+
+>seq0044
+EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWV
+WEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPM
+GAGFQAHLQK
+
+>seq0045
+FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGD
+YEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLW
+DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPME
+TGFKAHLNVR
+
+>seq0046
+INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLR
+LYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRF
+PAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
+
+>seq0047
+PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYM
+FDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEM
+RSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTY
+HLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYY
+TIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEG
+KIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
+
+>seq0048
+IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSM
+GRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQ
+AFQSAMKNGLKVVLK
+
+>seq0049
+IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRL
+YPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYP
+AFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
+
+>seq0050
+YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIF
+GTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKY
+IWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSA
+MKNGWKVTLE
+
+>seq0051
+YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNI
+FGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSK
+YIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPS
+AMKNGWKLDLK
+
+>seq0052
+MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLR
+TAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLC
+LGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
+
+>seq0053
+VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWEN
+ADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
+
+>seq0054
+IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGD
+EIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVA
+MFTNFKSFQAVPAAMDGGFKIHIH
+
+>seq0055
+IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGD
+EIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIA
+MFSQFKSFRTVPAAMDGGFNIYVE
+
+>seq0056
+IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLR
+LYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEI
+WPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
+
+>seq0057
+YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVD
+VFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGK
+LPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTV
+PAPFRNGFNIYLK
+
+>seq0058
+DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEA
+CLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPER
+FIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
+
+>seq0059
+LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
+AVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAP
+RICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
+
+>seq0060
+QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFET
+CSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARP
+FLETLKHAKRFCSIRERIESGE
+
+>seq0061
+ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEIN
+TLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAP
+WIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
+
+>seq0062
+YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTY
+ESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWE
+NPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNG
+FQVHLQPLHPTQN
+
+>seq0063
+DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKT
+LDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENP
+LQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLP
+MRIIPLSSSV
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/log
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/OG5_126554_0_preguidance/log
@ -0,0 +1,33 @@
+
+
+========================================= NEW GUIDANCE RUN STARTED ===========================================
+GUIDANCE COMMAND: perl guidance.v2.02/www/Guidance/guidance.pl --bootstraps 10 --seqFile batch2/OG5_126554_0_preguidance.fasta --msaProgram MAFFT --seqType aa --outDir /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance --seqCutoff 0.7 --colCutoff 0.4 --outOrder as_input --MSA_Param \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol
+Guidance::validate_Seqs(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/,Seqs.Orig.fas,AminoAcids,No): return: OK  Seqs.Orig.fas.FIXED 64
+Guidance::name2codeFastaFrom1(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED, /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes, /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas,0,seqNum);
+convert_fs_to_upper_case(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas)
+Align: mafft \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --amino  --quiet /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln
+Bootstrap_Trees: /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/../../programs/semphy/semphy -a 20 --jtt -H -J -v 8 --BPrepeats=10 -s /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln -o /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.out -T /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.outTree -l /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.log > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.std
+Guidance::pullOutBPtrees(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/,MSA,10,MAFFT);
+Guidance::root_BP_trees(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/,MSA, MAFFT, 10,"",BioPerl);
+Sample op according to uniform distribution: Guidance::SampleFromUnifomDist(1,3,/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//SampledOPVals.log,10)
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_0 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_0/MSA.MAFFT.semphy.tree_0.rooted.GoodBranchLength 19 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.000817428956 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_1 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_1/MSA.MAFFT.semphy.tree_1.rooted.GoodBranchLength 108 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.58462865668747 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_2 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_2/MSA.MAFFT.semphy.tree_2.rooted.GoodBranchLength 82 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.49936059497511 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_3 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_3/MSA.MAFFT.semphy.tree_3.rooted.GoodBranchLength 60 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.23331485380722 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_4 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_4/MSA.MAFFT.semphy.tree_4.rooted.GoodBranchLength 76 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.15783221114012 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_5 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_5/MSA.MAFFT.semphy.tree_5.rooted.GoodBranchLength 53 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.90590667209469 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_6 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_6/MSA.MAFFT.semphy.tree_6.rooted.GoodBranchLength 57 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.63676633992571 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_7 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_7/MSA.MAFFT.semphy.tree_7.rooted.GoodBranchLength 100 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.80645936921989 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_8 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_8/MSA.MAFFT.semphy.tree_8.rooted.GoodBranchLength 72 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.84405518368005 >> COS.std
+run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_9 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_9/MSA.MAFFT.semphy.tree_9.rooted.GoodBranchLength 24 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.13819830457351 >> COS.std
+calculating SP scores: /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/../../programs/msa_set_score/msa_set_score /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.aln /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.Guidance2 -d  /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/GUIDANCE2_MSA/ > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.msa_set_score.std
+Guidance::codes2name_scoresFile_NEW("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names");
+Guidance::removeLowSPsites_NoBioPerl ("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col",0.4,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.MSA.MAFFT.Removed_Col");
+REMOVED_SITES:0
+MSA_LENGTH:351
+ans=Convert_to_CSV("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv");
+ANS:OK
+Guidance::printColoredAlignment_With_CSS("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance_res_pair_res.html","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv",GUIDANCE2,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr");
+1Guidance::removeLowSPseq ("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq",0.7,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq");
+Guidance::make_Jalview_Color_MSA("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Features","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes");
+Guidance::make_Jalview_AnnotationGraph("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Annot","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv",GUIDANCE2." scores");
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/ScoreBySeq.tsv
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/ScoreBySeq.tsv
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/SummarizeRemovedSeqs.py
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/SummarizeRemovedSeqs.py
@ -0,0 +1,34 @@
+import os, sys
+from Bio import SeqIO
+from tqdm import tqdm
+
+
+prev_recs = [rec.id for rec in SeqIO.parse('AllCuratedNTDSeqs_020722_previous.fasta', 'fasta')]
+
+recs5 = { rec.id : file[:12] for file in os.listdir('Seq0.5') for rec in SeqIO.parse('Seq0.5/' + file, 'fasta') }
+recs7 = { rec.id : file[:12] for file in os.listdir('Seq0.5') for rec in SeqIO.parse('Seq0.7/' + file, 'fasta') }
+
+#print(len(prev_recs))
+print(recs5)
+#print(len(recs7))
+
+n_file = open('NumRemovedSeqs.csv', 'w')
+seqs5_file = open('AllRemovedSeqs_0.5.csv', 'w')
+seqs7_file = open('AllRemovedSeqs_0.7.csv', 'w')
+
+n_by_clade_5 = { }; n_by_clade_7 = { }
+for rec in prev_recs:
+	if(recs5[rec] not in n_by_clade_5):
+		n_by_clade_5.update({ recs5[rec] : 0 })
+		n_by_clade_7.update({ recs5[rec] : 0 })
+	if(rec not in recs5):
+		seqs5_file.write(rec + '\n')
+		n_by_clade_5[recs5[rec]] += 1
+	if(rec not in recs7):
+		seqs7_file.write(rec + '\n')
+		n_by_clade_7[recs5[rec]] += 1
+
+
+seqs5_file.close()
+
+
--- a/PTL2/Scripts-DEV/Guidance_EXAMPLE/get_nucl.py
+++ b/PTL2/Scripts-DEV/Guidance_EXAMPLE/get_nucl.py
@ -0,0 +1,11 @@
+import os, sys
+from Bio import SeqIO
+
+
+nucls = { rec.id : str(rec.seq) for rec in SeqIO.parse('AllCuratedNTDSeqs_020722_previous.fasta', 'fasta') }
+
+with open('AllCuratedNTDSeqs_022222_Seq0.7.fasta', 'w') as o:
+	for file in os.listdir('SeqFiltered_ToAlign/Preguidance_0.7_Aligned'):
+		if('.fas' in file):
+			for rec in SeqIO.parse('SeqFiltered_ToAlign/Preguidance_0.7_Aligned/' + file, 'fasta'):
+				o.write('>' + rec.id + '\n' + nucls[rec.id] + '\n\n')
--- a/PTL2/Scripts-DEV/pycache/guidance_treeBuilding.cpython-39.pyc
+++ b/PTL2/Scripts-DEV/pycache/guidance_treeBuilding.cpython-39.pyc
--- a/PTL2/Scripts-DEV/pycache/guidance_trees.cpython-39.opt-2.pyc
+++ b/PTL2/Scripts-DEV/pycache/guidance_trees.cpython-39.opt-2.pyc
--- a/PTL2/Scripts-DEV/pycache/guidance_trees.cpython-39.pyc
+++ b/PTL2/Scripts-DEV/pycache/guidance_trees.cpython-39.pyc
--- a/PTL2/Scripts-DEV/pycache/logger.cpython-39.pyc
+++ b/PTL2/Scripts-DEV/pycache/logger.cpython-39.pyc
--- a/PTL2/Scripts-DEV/pycache/preguidance.cpython-39.opt-2.pyc
+++ b/PTL2/Scripts-DEV/pycache/preguidance.cpython-39.opt-2.pyc
--- a/PTL2/Scripts-DEV/pycache/preguidance.cpython-39.pyc
+++ b/PTL2/Scripts-DEV/pycache/preguidance.cpython-39.pyc
--- a/PTL2/Scripts-DEV/pycache/utils.cpython-39.opt-2.pyc
+++ b/PTL2/Scripts-DEV/pycache/utils.cpython-39.opt-2.pyc
--- a/PTL2/Scripts-DEV/pycache/utils.cpython-39.pyc
+++ b/PTL2/Scripts-DEV/pycache/utils.cpython-39.pyc
--- a/PTL2/Scripts-DEV/contamination.py
+++ b/PTL2/Scripts-DEV/contamination.py
@ -0,0 +1,55 @@
+import os, sys, re
+import ete3
+from logger import Logger
+
+
+def get_best_clade(params, tree):
+
+	if params.target_taxa_file != None:
+		try:
+			target_taxa_list = [line.strip() for line in open(PathtoFiles + '/' + target_taxa_list)]
+		except (FileNotFoundError, TypeError):
+			Logger.Error('The --target_taxa_file could not be found or was incorrectly formatted.')
+
+	if params.at_least_file != None:
+		try:
+			at_least_list = [line.strip() for line in open(PathtoFiles + '/' + at_least_file)]
+		except (FileNotFoundError, TypeError):
+			Logger.Error('The --at_least_file could not be found or was incorrectly formatted.')
+	else:
+		at_least_list = []
+
+
+	### FROM HERE BELOW IN THIS FUNCTION NEEDS REPLACING WITH ETE3
+		
+	forbidden_nodes = [node for node in nodes_to_exclude]
+	for node in nodes_to_exclude:
+		for num in tree.getNodeNumsAbove(node):
+			forbidden_nodes.append(tree.node(num))
+	
+	best_node = None
+	best_size = 0
+	for node in tree.iterNodesNoRoot():
+		if(node not in forbidden_nodes):
+			leaves = tree.getAllLeafNames(node)
+							
+			num = 0.0; dem = 0.0;
+		
+			non_minor = []
+			for leaf in leaves:
+				if(leaf[:2] != target_minor and leaf[:4] != target_minor):
+					num += 1.0;
+					non_minor.append(leaf[:10])
+					
+			if(target_taxa_list == 'na' or target_taxa_list == '' or target_taxa_list == 'NA'):
+				n_targets = len(list(dict.fromkeys([tip[:10] for tip in leaves if(tip[:2] == target_clade or tip[:3] == target_clade or tip[:4] == target_clade or tip[:5] == target_clade or tip[:7] == target_clade or tip[:8] == target_clade)])))
+			else:
+				n_targets = len(list(dict.fromkeys([tip[:10] for tip in leaves if((tip[:2] == target_clade or tip[:3] == target_clade or tip[:4] == target_clade or tip[:5] == target_clade or tip[:7] == target_clade or tip[:8] == target_clade) and (tip[:10] in target_taxa_list or tip[:8] in target_taxa_list))])))
+							
+			at_least_taxa = len(list(dict.fromkeys([leaf[:10] for leaf in tree.getAllLeafNames(node) if leaf[:10] in at_least_list])))
+
+			if(num <= cont_num_contams and n_targets > best_size and n_targets >= min_presence and at_least_taxa >= num_at_least):
+				best_node = node
+				best_size = n_targets
+			
+	return best_node
--- a/PTL2/Scripts-DEV/guidance.v2.02/.DS_Store
+++ b/PTL2/Scripts-DEV/guidance.v2.02/.DS_Store
--- a/PTL2/Scripts-DEV/guidance.v2.02/Makefile
+++ b/PTL2/Scripts-DEV/guidance.v2.02/Makefile
@ -0,0 +1,33 @@
+.PHONY: all libs semphy programs clean install
+
+all: libs programs
+
+debug: libs.debug
+
+%: libs.% programs.%
+	echo $@
+
+libs: libs.all
+
+programs: programs.all
+
+programs.all: libs
+programs.debug: libs.debug
+
+semphy: programs.semphy
+
+install: programs.install
+
+programs.install programs.all semphy: libs
+
+clean: libs.clean programs.clean
+
+libs.%:
+	+cd libs;make $(*)
+
+programs.%:
+	+cd programs;make $(*)
+
+tags: libs/*/*.cpp libs/*/*.h programs/*/*.h programs/*/*.cpp
+	etags --members --language=c++ $^ 
+
--- a/PTL2/Scripts-DEV/guidance.v2.02/README
+++ b/PTL2/Scripts-DEV/guidance.v2.02/README
@ -0,0 +1,129 @@
+                GUIDANCE:  GUIDe tree based AligNment ConfidencE
+
+GUIDANCE is a software package for aligning biological sequences (DNA or
+amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating
+confidence scores for each column, sequence and residue in the alignment.
+
+URL: http://guidance.tau.ac.il/
+
+Authors: Osnat Penn, Eyal Privman, Haim Ashkenazy, Itamar Sela, Giddy Landan, Dan Graur, and Tal Pupko.
+
+When using the GUIDANCE2 algorithm please cite:
+-----------------------------------------------------------
+Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015)
+GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
+Nucleic Acids Research, 2015 Jul 1; 43: W7-W14.; doi: 10.1093/nar/gkq443
+
+Landan, G., and D. Graur. (2008).
+Local reliability measures from sets of co-optimal multiple sequence alignments.
+Pac Symp Biocomput 13:15-24
+
+When using the GUIDANCE algorithm please cite:
+-----------------------------------------------------------
+Penn, O., Privman, E., Landan, G., Graur, D. and Pupko, T. (2010).
+An alignment confidence score capturing robustness to guide-tree uncertainty. 
+Molecular Biology and Evolution, 2010 Aug;27(8):1759-67; doi:10.1093/molbev/msq066
+
+When using the HoT algorithm please cite:
+-----------------------------------------------------------
+Landan, G., and D. Graur. (2008).
+Local reliability measures from sets of co-optimal multiple sequence alignments.
+Pac Symp Biocomput 13:15-24
+
+Installation
+============
+
+  1. Unpack the archive by typing:
+        % tar -xzf guidance.v2.01.tgz
+
+  2. Compile the package by typing:
+        % cd guidance.v2.01
+        % make
+     (Running `make' takes a while)
+
+  3. Check if you have the desired alignment program installed:
+
+     MAFFT: Type "mafft" and check that you have version 6.712 or newer.
+      * Else download and install MAFFT from:  http://mafft.cbrc.jp/alignment/software/
+
+     PRANK: Type "prank" and check that you have it insalled
+      * Else download and install PRANK from:  http://www.ebi.ac.uk/goldman-srv/prank/prank/
+
+     CLUSTALW: Type "clustalw" and check that you have it insalled
+      * Else download and install CLUSTALW from:  http://www.ebi.ac.uk/Tools/clustalw2/index.html
+
+     MUSCLE: Type "muscle" and check that you have it insalled
+      * Else download and install MUSCLE from:  http://www.drive5.com/muscle/index.htm
+
+	 PAGAN: Type "pagan" and check that you have it installed
+      * Else download and install PAGAN from:  http://code.google.com/p/pagan-msa/
+      * In case PAGAN is used not for user provided alignment (using --msaFile), mafft is also required to be installed.
+
+
+  4. GUIDANCE also uses Perl, BioPerl and Ruby:
+                * Type "perl -v" and check that you Perl installed.
+                        Else download and install it from: http://www.perl.org/
+                * Type "perl -e 'use Bio::SeqIO'" to check that you have BioPerl.
+                        Else download and install it from: http://www.bioperl.org/
+                * Type "ruby -version" to check that you have ruby.
+                        Else download and install it from: http://www.ruby-lang.org/en/
+
+Usage
+=====
+
+Run the Perl script: guidance.v2.01/www/Guidance/guidance.pl
+(Note that you cannot move this script out of its directory, because it uses relative paths to other files in other directories. Sorry)
+GUIDANCE uses flags in the command line arguments: (for help, type: "perl guidance")
+
+USAGE:perl guidance.pl --seqFile SEQFILE --msaProgram [MAFFT|PRANK|CLUSTALW|MUSCLE] --seqType [aa|nuc|codon] --outDir FULL_PATH_OUTDIR
+
+Required parameters:
+  --seqFile          Input sequence file in FASTA format
+  --seqType      Sequence type may be either of: nuc (nucleotides), aa (amino acids),
+                 or codon (nucleotides that will be treated as whole codons)
+  --msaProgram   The alignment program - may be either MAFFT, PRANK, CLUSTALW or  MUSCLE
+  --outDir       The output directory were all output files will be created [please provide full and not relative path]
+                 (will be created automatically)
+
+Optional parameters:
+  --program      The confidence measure may be GUIDANCE2, GUIDANCE or HoT. default=GUIDANCE2
+  --bootstraps   Number of bootstrap iterations. default=100
+  --genCode      Genetic code for use in codon sequence. default=1
+                 1>  Nuclear Standard
+                 15> Nuclear Blepharisma
+                 6>  Nuclear Ciliate
+                 10> Nuclear Euplotid
+                 2>  Mitochondria Vertebrate
+                 5>  Mitochondria Invertebrate
+                 3>  Mitochondria Yeast
+                 13> Mitochondria Ascidian
+                 9>  Mitochondria Echinoderm
+                 14> Mitochondria Flatworm
+                 4>  Mitochondria Protozoan
+  --outOrder     May be either aligned or as_input. default=aligned
+  --msaFile      Input alignment file - not recommended, see documentation online at: guidance.tau.ac.il
+  --seqCutoff    Sequence confidence cutoff between 0 to 1. default=0.6
+  --colCutoff    Columnd confidence cutoff between 0 to 1. default=0.93
+  --mafft        Path to mafft executable. default=mafft
+  --prank        Path to prank executable. default=prank
+  --clustalw     path to clustalw executable. default=clustalw
+  --muscle       path to muscle executable. default=muscle
+  --pagan        path to pagan executable. default=pagan
+  --ruby         path to ruby executable. default=ruby
+  --dataset      Unique name for the Dataset - will be used as prefix to outputs (default=MSA)
+  --MSA_Param:   Passing parameters for the alignment program e.g -F to prank. To pass parameter containning '-' in it, add \ before each '-' e.g. \-F for PRANK
+  --proc_num:    Number of processors to use (default=1)
+
+EXAMPLES:
+
+>perl guidance.pl --seqFile protein.fas --msaProgram MAFFT --seqType aa --outDir /somedir/protein.guidance
+Will align the amino acid sequences in the fasta file "protein.fas" using MAFFT and output all results to the diretory "/somedir/protein.guidance"
+
+>perl guidance.pl --seqFile codingSeq.fas --msaProgram PRANK --seqType codon --outDir /somedir/codingSeq.guidance --genCode 2 --bootstraps 30
+Will align the codon sequences in the fasta file "codingSeq.fas" using PRANK after translation using the vertebrate mitochondrial genetic code and output all results to the diretory "/somedir/codingSeq.guidance". Only 30 bootstrap iterations will be done instead of the default 100 (cut run-time by a factor of 3)
+
+Copyrights
+==========
+
+    * To modify the code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko: talp@post.tau.ac.il
+    * Please note that the use of the GUIDANCE program is for academic use only
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/Makefile
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/Makefile
@ -0,0 +1,29 @@
+#	$Id: Makefile 942 2006-10-18 12:28:12Z ninio $	
+
+# There might be need for a split (as done in programs/Makefile) becouse of a bug in make 3.80.1 - see 
+# http://www.cygwin.com/ml/cygwin/2004-09/msg01659.html
+
+LIBS= phylogeny
+
+# all has to be the FIRST task!
+TASKS= all clean test depend debug All install doubleRep
+.PHONY: $(TASKS) $(LIBS)
+
+ define TASKS_template
+    $(1): $$(addsuffix .$(1),$(LIBS))
+ endef
+
+$(foreach task,$(TASKS),$(eval $(call TASKS_template,$(task))))
+
+define LIB_template
+   $(1).%:
+	+cd $(1) && make $$(*)
+endef
+
+$(foreach lib,$(LIBS),$(eval $(call LIB_template,$(lib))))
+
+
+
+$(LIBS):
+	+cd $@ && make 
+
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/.project
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/.project
@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>phylogeny</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+			<triggers>clean,full,incremental,</triggers>
+			<arguments>
+				<dictionary>
+					<key>?name?</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.append_environment</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildArguments</key>
+					<value></value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildCommand</key>
+					<value>make</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.buildLocation</key>
+					<value>${workspace_loc:/phylogeny/Debug}</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
+					<value>clean</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.contents</key>
+					<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
+					<value>false</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.enableFullBuild</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
+					<value>all</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.stopOnError</key>
+					<value>true</value>
+				</dictionary>
+				<dictionary>
+					<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
+					<value>true</value>
+				</dictionary>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.cdt.core.ccnature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.eclipse.cdt.core.cnature</nature>
+	</natures>
+</projectDescription>
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/AddLog.cpp
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/AddLog.cpp
@ -0,0 +1,25 @@
+// $Id: AddLog.cpp 962 2006-11-07 15:13:34Z privmane $
+
+// version 1.00
+// last modified 3 Nov 2002
+
+#include "AddLog.h"
+#include <cmath>
+
+const int tAddLog_Precompute::G_LOGADD = 500;
+const int tAddLog_Precompute::D_LOGADD = 50;
+
+tAddLog_Precompute AddLogData;
+
+int tAddLog_Precompute::d_logadd;
+
+tAddLog_Precompute::tAddLog_Precompute(){
+  d_logadd = int(D_LOGADD*log(10.0)*G_LOGADD);
+  logaddf = new double [d_logadd+1];
+  for (int i=0; i<= d_logadd; i++)
+    logaddf[i] = log(1.0+exp(-static_cast<double>(i)/G_LOGADD));
+}
+
+tAddLog_Precompute::~tAddLog_Precompute(){
+  delete [] logaddf;
+}
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/AddLog.h
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/AddLog.h
@ -0,0 +1,67 @@
+// $Id: AddLog.h 962 2006-11-07 15:13:34Z privmane $
+
+// version 1.00
+// last modified 2 Nov 2002
+
+#ifndef __AddLog_h
+#define __AddLog_h
+
+#include <iostream>
+using namespace std;
+
+class tAddLog_Precompute {
+  public:
+
+  tAddLog_Precompute();
+  ~tAddLog_Precompute();
+
+  double AddLog( double x, double y );
+  
+private:
+  static const int D_LOGADD; // = 50;   // y/x < 1e-D discard
+  static const int G_LOGADD;// = 500;  // step function look-up every 1/G
+  static int d_logadd;
+
+  double *logaddf;
+};
+
+extern tAddLog_Precompute AddLogData;
+
+inline
+double
+AddLog(double x, double y ){
+  return AddLogData.AddLog(x, y);
+}
+
+inline double
+tAddLog_Precompute::AddLog(double x, double y ){
+  if (x < y)  {
+    double dummy = x;
+    x = y;
+    y = dummy;
+  }
+
+#ifdef notdef  
+  return x + log(1 + exp(y-x));
+#endif
+  
+  double z = (x-y)*G_LOGADD;
+  int i = int(z);
+  if( i < d_logadd ) x += ((i+1-z)*logaddf[i] + (z-i)*logaddf[i+1]);
+  return x;
+}
+
+#endif
+
+
+/*
+Folks,
+
+In many of our program we use the AddLog procedure that compute the sum of
+two numbers in log form. Gill spent some time investigating faster versions
+of this procedure, which gave him 3-4 fold speedup on his program. Attached
+is my re-packaging of his solution. I think it will be useful in some of the
+code we use.
+
+-Nir
+*/
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/AddLog.o
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/AddLog.o
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/C_evalParamUSSRV.cpp
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/C_evalParamUSSRV.cpp
@ -0,0 +1,112 @@
+// 	$Id: C_evalParamUSSRV.cpp 1915 2007-04-04 15:56:24Z privmane $	
+#include "C_evalParamUSSRV.h"
+
+// *********************
+// *       USSRV       *
+// *********************
+
+MDOUBLE C_evalParamUSSRV::operator() (MDOUBLE param) {
+		
+		setParam(param);
+		MDOUBLE res = likelihoodComputation2USSRV::getTreeLikelihoodAllPosAlphTheSame(_et,_sc,_baseSc,*_pModel,_weights);
+		print(param,res);
+		return -res;
+}
+
+void C_evalAlphaUSSRV::setParam(MDOUBLE alpha)
+{
+	if (_pModel->noOfCategor() == 1)
+		errorMsg::reportError(" one category when trying to optimize alpha");
+	_pModel->updateAlpha(alpha);	
+}
+
+void C_evalAlphaUSSRV::print(MDOUBLE alpha,MDOUBLE res) {
+			LOG(5,<<" with Alpha = "<<alpha<<" logL = " <<res<<endl);
+}
+
+
+void C_evalNuUSSRV::setParam(MDOUBLE Nu)
+{
+	_pModel->updateNu(Nu);
+}
+
+void C_evalNuUSSRV::print(MDOUBLE nu,MDOUBLE res) {
+	LOG(5,<<" with Nu = "<<nu<<" logL = " <<res<<endl);
+}
+
+void C_evalFUSSRV::setParam(MDOUBLE f)
+{
+	_pModel->updateF(f);
+}
+
+void C_evalFUSSRV::print(MDOUBLE f,MDOUBLE res) {
+	LOG(5,<<" with F = "<<f<<" logL = " <<res<<endl);
+}
+
+
+// *********************
+// *       SSRV       *
+// *********************
+
+MDOUBLE C_evalParamSSRV::operator() (MDOUBLE param) {
+
+	setParam(param);
+	MDOUBLE res = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_et,_sc,_ssrvSp,_weights);
+	print(param,res);
+	return -res;
+}
+
+void C_evalAlphaSSRV::setParam(MDOUBLE alpha)
+{
+	if (alpha<0) 
+		errorMsg::reportError("ERROR in C_evalAlphaSSRV::setParam, alpha is < 0 ");
+		
+	replacementModelSSRV* pMulRM = static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel());
+	gammaDistribution* gammaDist = static_cast<gammaDistribution*>(pMulRM->getDistribution()); 
+	gammaDist->setAlpha(alpha);
+	pMulRM->updateQ();
+}
+
+void C_evalAlphaSSRV::print(MDOUBLE alpha,MDOUBLE res) {
+	LOG(5,<<" with Alpha = "<<alpha<<" logL = " <<res<<endl);
+}
+
+
+void C_evalNuSSRV::setParam(MDOUBLE Nu)
+{
+	if (Nu<0) 
+		errorMsg::reportError("C_evalNuSSRV::setParam, nu is < 0 ");
+		
+	static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel())->setRateOfRate(Nu);
+}
+
+void C_evalNuSSRV::print(MDOUBLE nu,MDOUBLE res) {
+	LOG(5,<<" with Nu = "<<nu<<" logL = " <<res<<endl);
+}
+
+void C_evalTrTvSSRV::setParam(MDOUBLE TrTv)
+{
+	replacementModelSSRV* pMulRM = static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel());
+	static_cast<tamura92*>(pMulRM->getBaseRM())->changeTrTv(TrTv);
+	pMulRM->updateQ();
+}
+
+void C_evalTrTvSSRV::print(MDOUBLE TrTv,MDOUBLE res) {
+	LOG(5,<<" with TrTv = "<<TrTv<<" logL = " <<res<<endl);
+}
+
+void C_evalThetaSSRV::setParam(MDOUBLE Theta)
+{
+	replacementModelSSRV* pMulRM = static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel());
+	static_cast<tamura92*>(pMulRM->getBaseRM())->changeTheta(Theta);
+	pMulRM->updateFreq();
+	pMulRM->updateQ();
+}
+
+void C_evalThetaSSRV::print(MDOUBLE Theta,MDOUBLE res) {
+	LOG(5,<<" with Theta = "<<Theta<<" logL = " <<res<<endl);
+}
+
+
+
+
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/C_evalParamUSSRV.h
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/C_evalParamUSSRV.h
@ -0,0 +1,177 @@
+// 	$Id: C_evalParamUSSRV.h 1915 2007-04-04 15:56:24Z privmane $	
+#ifndef ___C_EVAL_PARAM_USSRV
+#define ___C_EVAL_PARAM_USSRV
+
+#include "definitions.h"
+
+#include "likelihoodComputation.h"
+#include "likelihoodComputation2USSRV.h"
+#include "sequenceContainer.h"
+#include "stochasticProcess.h"
+#include "gammaDistribution.h"
+#include "tree.h"
+#include "replacementModelSSRV.h"
+#include "tamura92.h"
+#include "stochasticProcessSSRV.h"
+#include "ussrvModel.h"
+#include "logFile.h"
+
+// *********************
+// *       USSRV       *
+// *********************
+
+class C_evalParamUSSRV {
+public:
+	C_evalParamUSSRV(const tree& et,
+				const sequenceContainer& sc,
+				const sequenceContainer& baseSc,
+				ussrvModel* pModel,
+				const Vdouble* weights = NULL)
+    : _et(et),_sc(sc),_baseSc(baseSc),_pModel(pModel),_weights(weights){}
+
+	MDOUBLE operator() (MDOUBLE param) ;
+    virtual ~C_evalParamUSSRV(){}
+
+protected:
+	const tree& _et;
+	const sequenceContainer& _sc;
+	const sequenceContainer& _baseSc;
+	ussrvModel* _pModel;
+	const Vdouble * _weights;
+
+
+protected:
+	virtual void setParam(MDOUBLE param) = 0;
+	virtual void print(MDOUBLE param,MDOUBLE res) =0;
+};
+
+
+class C_evalAlphaUSSRV : public C_evalParamUSSRV {
+public:
+  C_evalAlphaUSSRV(const tree& et,
+				const sequenceContainer& sc,
+				const sequenceContainer& baseSc,
+				ussrvModel* pModel,
+				const Vdouble *weights = NULL) 
+				 : C_evalParamUSSRV(et,sc,baseSc,pModel,weights) 
+				{}
+  
+protected:
+	virtual void setParam(MDOUBLE alpha);
+	virtual void print(MDOUBLE alpha,MDOUBLE res);
+};
+
+
+
+class C_evalNuUSSRV : public C_evalParamUSSRV{
+public:
+  C_evalNuUSSRV(	const tree& et,
+				const sequenceContainer& sc,
+				const sequenceContainer& baseSc,
+				ussrvModel* pModel,
+				const Vdouble * weights = NULL)
+    : C_evalParamUSSRV(et,sc,baseSc,pModel,weights){}
+
+protected:
+	virtual void setParam(MDOUBLE Nu);
+	virtual void print(MDOUBLE nu,MDOUBLE res);
+};
+
+class C_evalFUSSRV : public C_evalParamUSSRV{
+public:
+  C_evalFUSSRV(	const tree& et,
+				const sequenceContainer& sc,
+				const sequenceContainer& baseSc,
+				ussrvModel* pModel,
+				const Vdouble * weights = NULL)
+    : C_evalParamUSSRV(et,sc,baseSc,pModel,weights){}
+
+protected:
+	virtual void setParam(MDOUBLE F);
+	virtual void print(MDOUBLE f,MDOUBLE res);
+};
+
+// *********************
+// *       SSRV        *
+// *********************
+
+class C_evalParamSSRV {
+public:
+	C_evalParamSSRV(const tree& et,
+		const sequenceContainer& sc,
+		stochasticProcessSSRV& ssrvSp,
+		const Vdouble* weights = NULL)
+		: _et(et),_sc(sc),_ssrvSp(ssrvSp),_weights(weights){}
+
+		MDOUBLE operator() (MDOUBLE param) ;
+		virtual ~C_evalParamSSRV(){}
+
+protected:
+	const tree& _et;
+	const sequenceContainer& _sc;
+	stochasticProcessSSRV& _ssrvSp;
+	const Vdouble * _weights;
+
+
+protected:
+	virtual void setParam(MDOUBLE param) = 0;
+	virtual void print(MDOUBLE param,MDOUBLE res) =0;
+};
+
+
+class C_evalAlphaSSRV : public C_evalParamSSRV {
+public:
+	C_evalAlphaSSRV(const tree& et,
+		const sequenceContainer& sc,
+		stochasticProcessSSRV& ssrvSp,
+		const Vdouble *weights = NULL) 
+		: C_evalParamSSRV(et,sc,ssrvSp,weights) 
+	{}
+
+protected:
+	virtual void setParam(MDOUBLE alpha);
+	virtual void print(MDOUBLE alpha,MDOUBLE res);
+};
+
+
+
+class C_evalNuSSRV : public C_evalParamSSRV{
+public:
+	C_evalNuSSRV(	const tree& et,
+		const sequenceContainer& sc,
+		stochasticProcessSSRV& ssrvSp,
+		const Vdouble * weights = NULL)
+		: C_evalParamSSRV(et,sc,ssrvSp,weights){}
+
+protected:
+	virtual void setParam(MDOUBLE Nu);
+	virtual void print(MDOUBLE nu,MDOUBLE res);
+};
+
+class C_evalTrTvSSRV : public C_evalParamSSRV{
+public:
+	C_evalTrTvSSRV(const tree& et,
+		const sequenceContainer& sc,
+		stochasticProcessSSRV& ssrvSp,
+		const Vdouble * weights = NULL)
+		: C_evalParamSSRV(et,sc,ssrvSp,weights){}
+
+protected:
+	virtual void setParam(MDOUBLE TrTv);
+	virtual void print(MDOUBLE TrTv,MDOUBLE res);
+};
+
+class C_evalThetaSSRV : public C_evalParamSSRV{
+public:
+	C_evalThetaSSRV(const tree& et,
+		const sequenceContainer& sc,
+		stochasticProcessSSRV& ssrvSp,
+		const Vdouble * weights = NULL)
+		: C_evalParamSSRV(et,sc,ssrvSp,weights){}
+
+protected:
+	virtual void setParam(MDOUBLE Theta);
+	virtual void print(MDOUBLE Theta,MDOUBLE res);
+};
+
+#endif
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/C_evalParamUSSRV.o
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/C_evalParamUSSRV.o
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/ConversionUtils.cpp
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/ConversionUtils.cpp
@ -0,0 +1,52 @@
+#include "ConversionUtils.h"
+#include "someUtil.h"
+#include "errorMsg.h"
+
+#include <cmath>
+
+using namespace std;
+
+void appendIntToString (string& ioString, const int inValue) {
+	std::ostringstream o;
+	o << ioString<< inValue;
+	ioString = o.str();
+}
+
+string appendInt2string(const int x)
+{
+	string res;
+	appendIntToString(res, x);
+	return res;
+}
+
+string appendDouble2string(const double x, const int lenght){
+	
+	// first getting the integer part:
+	int theIntegerPart = static_cast<int>(x);
+	double theRemainingPart = fabs(x-theIntegerPart);
+	int integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght));
+	string part1, part2; 
+	appendIntToString(part1, theIntegerPart);
+	appendIntToString(part2, integerRepresentingTheRemainingPart);
+	while (part2.length()<lenght){
+		part2.insert(0, "0");
+	}
+
+	string result = part1;
+	result += ".";
+	result += part2;
+
+	// removing 0 from the end
+	int i = result.length()-1;
+	while (result[i]!='.' && i>0 && result[i]=='0'){
+		result.erase(i);
+		i--;
+	}
+	
+	// removing "." if this is the last character in the string.
+	if (result[result.length()-1]=='.')
+	result.erase(result.length()-1);
+
+	return result;
+}
+
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/ConversionUtils.h
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/ConversionUtils.h
@ -0,0 +1,51 @@
+//utility class that converts between data types
+#ifndef ___ConversionUtils_h
+#define ___ConversionUtils_h
+
+#include <sstream>
+#include <string>
+#include "definitions.h"
+
+using namespace std;
+
+//a function that turns an integer to string 
+
+void appendIntToString (string& ioString, const int inValue);
+string appendDouble2string(const double x, int const howManyDigitsAfterTheDot=5);
+string appendInt2string(const int x);
+
+
+// Trims spaces at the left side of a string
+static inline string trim_left(const string& str )
+{
+	int i=str.find_first_not_of(" \t");
+	if(str.size()==0 || i >= str.size())
+		return str;
+	return str.substr( i ) ;
+}
+ 
+
+////
+// Trims spaces at the right side of a string
+static inline string trim_right(const string& str )
+{
+	int i=str.find_last_not_of(" \t");
+	if(str.size()==0 || i >= str.size())
+		return str;
+	return str.substr(0, i + 1);
+}
+  
+//// 
+// Trims spaces at both sides of a string
+static inline string trim(const string& str )
+{
+	return trim_left(trim_right(str));
+}
+
+
+#endif
+
+
+
+
+
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/ConversionUtils.o
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/ConversionUtils.o
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GLaguer.cpp
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GLaguer.cpp
@ -0,0 +1,178 @@
+// $Id: GLaguer.cpp 962 2006-11-07 15:13:34Z privmane $
+#include "definitions.h"
+#include "GLaguer.h"
+
+#include "errorMsg.h"
+#include "gammaUtilities.h"
+
+
+
+GLaguer::GLaguer(const int pointsNum, const MDOUBLE alf, Vdouble & points, Vdouble & weights)
+{
+	gaulag(_points, _weights, alf, pointsNum);
+
+	weights = _weights;
+	points = _points;
+}
+
+
+//Input: alf = the alpha parameter of the Laguerre polynomials
+//		 pointsNum = the polynom order
+//Output: the abscissas and weights are stored in the vecotrs x and w, respectively. 
+//Discreption: given alf, the alpha parameter of the Laguerre polynomials, the function returns the abscissas and weights
+//			   of the n-point Guass-Laguerre quadrature formula.
+//			   The smallest abscissa is stored in x[0], the largest in x[pointsNum - 1].
+void GLaguer::gaulag(Vdouble &x, Vdouble  &w, const MDOUBLE alf, const int pointsNum)
+{
+	x.resize(pointsNum, 0.0);
+	w.resize(pointsNum, 0.0);
+	const int MAXIT=10000;
+	const MDOUBLE EPS=1.0e-6;
+	int i,its,j;
+	MDOUBLE ai,p1,p2,p3,pp,z=0.0,z1;
+
+	int n= x.size();
+	for (i=0;i<n;i++) {
+		//loops over the desired roots
+		if (i == 0) { //initial guess for the smallest root
+			z=(1.0+alf)*(3.0+0.92*alf)/(1.0+2.4*n+1.8*alf);
+		} else if (i == 1) {//initial guess for the second smallest root
+			z += (15.0+6.25*alf)/(1.0+0.9*alf+2.5*n);
+		} else { //initial guess for the other roots
+			ai=i-1;
+			z += ((1.0+2.55*ai)/(1.9*ai)+1.26*ai*alf/
+				(1.0+3.5*ai))*(z-x[i-2])/(1.0+0.3*alf);
+		}
+		for (its=0;its<MAXIT;its++) { //refinement by Newton's method
+			p1=1.0;
+			p2=0.0;
+			for (j=0;j<n;j++) { //Loop up the recurrence relation to get the Laguerre polynomial evaluated at z.
+				p3=p2;
+				p2=p1;
+				p1=((2*j+1+alf-z)*p2-(j+alf)*p3)/(j+1);
+			}
+			//p1 is now the desired Laguerre polynomial. We next compute pp, its derivative,
+			//by a standard relation involving also p2, the polynomial of one lower order.
+			pp=(n*p1-(n+alf)*p2)/z;
+			z1=z;
+			z=z1-p1/pp; //Newton's formula
+			if (fabs(z-z1) <= EPS) 
+				break;
+		}
+		if (its >= MAXIT) 
+			errorMsg::reportError("too many iterations in gaulag");
+		x[i]=z;
+		w[i] = -exp(gammln(alf+n)-gammln(MDOUBLE(n)))/(pp*n*p2);
+	}
+}
+
+
+void GLaguer::GetPhylipLaguer(const int categs, MDOUBLE alpha, Vdouble & points, Vdouble & weights)
+{
+  /* calculate rates and probabilities to approximate Gamma distribution
+     of rates with "categs" categories and shape parameter "alpha" using
+     rates and weights from Generalized Laguerre quadrature */
+
+	points.resize(categs, 0.0);
+	weights.resize(categs, 0.0);
+	long i;
+	raterootarray lgroot; /* roots of GLaguerre polynomials */
+	double f, x, xi, y;
+
+	alpha = alpha - 1.0;
+	lgroot[1][1] = 1.0+alpha;
+	for (i = 2; i <= categs; i++)
+	{
+		cerr<<lgroot[i][1]<<"\t";
+		lgr(i, alpha, lgroot);                   /* get roots for L^(a)_n */
+		cerr<<lgroot[i][1]<<endl;
+	}
+	/* here get weights */
+	/* Gamma weights are (1+a)(1+a/2) ... (1+a/n)*x_i/((n+1)^2 [L_{n+1}^a(x_i)]^2)  */
+	f = 1;
+	for (i = 1; i <= categs; i++)
+		f *= (1.0+alpha/i);
+	for (i = 1; i <= categs; i++) {
+		xi = lgroot[categs][i];
+		y = glaguerre(categs+1, alpha, xi);
+		x = f*xi/((categs+1)*(categs+1)*y*y);
+		points[i-1] = xi/(1.0+alpha);
+		weights[i-1] = x;
+	}
+}
+
+
+void GLaguer::lgr(long m, double alpha, raterootarray lgroot)
+{ /* For use by initgammacat.  Get roots of m-th Generalized Laguerre
+     polynomial, given roots of (m-1)-th, these are to be
+     stored in lgroot[m][] */
+	long i;
+	double upper, lower, x, y;
+	bool dwn;   /* is function declining in this interval? */
+
+	if (m == 1) {
+		lgroot[1][1] = 1.0+alpha;
+	} else {
+		dwn = true;
+		for (i=1; i<=m; i++) {
+			if (i < m) {
+				if (i == 1)
+					lower = 0.0;
+				else
+					lower = lgroot[m-1][i-1];
+				upper = lgroot[m-1][i];
+			} 
+			else { /* i == m, must search above */
+				lower = lgroot[m-1][i-1];
+				x = lgroot[m-1][m-1];
+				do {
+					x = 2.0*x;
+					y = glaguerre(m, alpha,x);
+				}	while ((dwn && (y > 0.0)) || ((!dwn) && (y < 0.0)));
+				upper = x;
+			}
+			while (upper-lower > 0.000000001) {
+				x = (upper+lower)/2.0;
+				if (glaguerre(m, alpha, x) > 0.0) {
+					if (dwn)
+						lower = x;
+					else
+						upper = x;
+				} 
+				else {
+					if (dwn)
+						upper = x;
+					else
+						lower = x;
+				}			 
+			}
+			lgroot[m][i] = (lower+upper)/2.0;
+			dwn = !dwn; // switch for next one 
+		}
+	}
+} /* lgr */
+
+
+double GLaguer::glaguerre(long m, double b, double x)
+{ /* Generalized Laguerre polynomial computed recursively.
+     For use by initgammacat */
+	long i;
+	double gln, glnm1, glnp1; /* L_n, L_(n-1), L_(n+1) */
+
+	if (m == 0)
+		return 1.0;
+	else {
+		if (m == 1)
+		return 1.0 + b - x;
+		else {
+			gln = 1.0+b-x;
+			glnm1 = 1.0;
+			for (i=2; i <= m; i++) {
+				glnp1 = ((2*(i-1)+b+1.0-x)*gln - (i-1+b)*glnm1)/i;
+				glnm1 = gln;
+				gln = glnp1;
+			}
+		return gln;
+		}
+	}
+} /* glaguerre */
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GLaguer.h
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GLaguer.h
@ -0,0 +1,30 @@
+// $Id: GLaguer.h 962 2006-11-07 15:13:34Z privmane $
+#ifndef ___GLAGUER
+#define ___GLAGUER
+
+#include "definitions.h"
+#include <vector>
+using namespace std;
+
+typedef double raterootarray[35][35];
+
+class GLaguer
+{
+public:
+	explicit GLaguer(const int pointsNum, const MDOUBLE alpha, Vdouble & points, Vdouble & weights);
+	
+	void GetPhylipLaguer(const int pointsNum, MDOUBLE alf, Vdouble & points, Vdouble & weights);
+
+private:
+	void gaulag(Vdouble &x, Vdouble  &w, const MDOUBLE alf, const int pointsNum);
+	
+	void lgr(long m, double alpha, raterootarray lgroot);
+	double glaguerre(long m, double b, double x);
+
+
+private:
+	Vdouble _points;
+	Vdouble _weights;
+};
+
+#endif
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GLaguer.o
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GLaguer.o
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GamMixtureOptimizer.cpp
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GamMixtureOptimizer.cpp
@ -0,0 +1,156 @@
+#include "GamMixtureOptimizer.h"
+#include "someUtil.h"
+#include "optGammaMixtureEM.h"
+#include "optGammaMixtureLS.h"
+
+#include <fstream>
+#include <algorithm>
+#include <ctime>
+using namespace std;
+
+
+
+GamMixtureOptimizer::GamMixtureOptimizer(stochasticProcess* pSp, const sequenceContainer& sc, const tree& inTree, unObservableData* unObservableData_p)
+{
+	_pSc = &sc;
+	_pTree = &inTree;
+	_pSp = pSp;
+	_unObservableData_p = unObservableData_p;
+	_tolOptSpecific = 0.001;
+
+}
+
+
+GamMixtureOptimizer::~GamMixtureOptimizer()
+{
+}
+
+
+///////////////////////////////////////////////////////////////////////////////////////////////////////////
+//findBestParamManyStarts: Finds the best gammaMixture from many starting points.
+//The function starts form few starting points. 
+//For each point it tries to optimize the likellihood doing only a small number of iterations.
+//It then picks the best points (highest likelihood) and continue the maximization for these points only.
+//This can be repeated a number of times, each cycle with a different optimization algorithm.
+//The best gammaMixture is stored in _sp and the best likelihood is returned.
+//input Parameters:
+//pointsNum: a vector with the number of points to peformed the current cycle of optimization.
+//iterNum: the number of iterations to perform in each cycle.
+//OptAlgs: the optimization algorithm to be performed in each cycle.
+//tol        = for determining convergence in the maximization process. 
+MDOUBLE GamMixtureOptimizer::findBestParamManyStarts(const Vint pointsNum, const Vint iterNum, const vector<OptimAlg> OptAlgs, const Vdouble tols, const Vdouble * pWeights, ofstream* pOutF/*= NULL*/)
+{
+	//make sure that the number of points in each cycle is not bigger than the previous cycle.
+	int i;	
+	for (i = 0; i < pointsNum.size()-1; ++i)
+	{
+		if (pointsNum[i] < pointsNum[i+1])
+			errorMsg::reportError("input error in GamMixtureOptimizer::findBestParamManyStarts()");
+	}
+
+	//create starting distributions 
+	vector<mixtureDistribution*> distVec;
+	const mixtureDistribution * pMixture = getMixtureDist();
+	for (i = 0; i < pointsNum[0]; ++i)
+	{
+		//the first distribution will be the current one
+		if (i == 0)
+			distVec.push_back(new mixtureDistribution(*pMixture)); 
+		else
+			distVec.push_back(new mixtureDistribution(pMixture->getComponentsNum(), pMixture->categoriesForOneComponent(), LAGUERRE, 15, 15)); 
+	}
+
+	//make a small number of iterations for all random starts 
+	int numOfOptCycles = pointsNum.size();
+	Vdouble likelihoodVec;
+	for (i = 0; i < numOfOptCycles; ++i)
+	{
+		if (i != 0)
+		{
+			vector<mixtureDistribution*> tmpDistVec(0);
+			//sort results and continue optimization only with the best (pointsNum[i]) points
+			Vdouble sortedL = likelihoodVec;
+			sort(sortedL.begin(),sortedL.end());
+			MDOUBLE threshold = sortedL[sortedL.size()- pointsNum[i]];
+			for (int j = 0; j < likelihoodVec.size(); ++j)
+			{
+				if (likelihoodVec[j] >= threshold) 
+					tmpDistVec.push_back(distVec[j]);
+				else
+					delete distVec[j];
+			}
+			distVec.clear();
+			distVec = tmpDistVec;
+		} 
+		
+		likelihoodVec.clear();
+		likelihoodVec.resize(pointsNum[i]); 
+		int c; 		
+		for (c = 0; c < pointsNum[i]; ++c)
+		{
+			cerr <<"optimizing point " <<c<<endl;
+			MDOUBLE ll = optimizeParam(distVec[c], iterNum[i], OptAlgs[i], tols[i], pWeights, pOutF);
+			cerr<<"pointi: "<<c<<"  likelihood = "<<ll<<endl;
+			likelihoodVec[c] = ll;
+		}
+	}
+
+	Vdouble sortedL = likelihoodVec;
+	sort(sortedL.begin(),sortedL.end());
+	MDOUBLE bestL = sortedL[likelihoodVec.size() - 1];
+	for (i = 0; i < likelihoodVec.size(); ++i)
+	{
+		if (bestL == likelihoodVec[i]) 
+		{
+			_pSp->setDistribution(distVec[i]);
+		}
+		delete distVec[i];
+	}	
+	distVec.clear();
+	return bestL;
+}
+
+MDOUBLE GamMixtureOptimizer::findBestParam(const OptimAlg alg, const int maxIterations, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF)
+{
+	mixtureDistribution* pInDistribution = static_cast<mixtureDistribution*>(_pSp->distr());
+	return optimizeParam(pInDistribution, maxIterations, alg, tol, pWeights, pOutF);
+}
+
+
+MDOUBLE GamMixtureOptimizer::optimizeParam(mixtureDistribution* pInDistribution, const int maxIterations, const OptimAlg alg, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF)
+{
+	MDOUBLE res = 0.0;
+	switch (alg)
+	{
+	case EM: {
+		optGammaMixtureEM emOpt(*_pSp, *_pSc, *_pTree); 
+		res = emOpt.optimizeParam(pInDistribution, maxIterations, tol, _tolOptSpecific, pOutF);
+		break;
+		}
+	case ONE_DIM: {
+		optGammaMixtureLS lsOpt(_pSp, *_pSc, *_pTree,MAXIMUM_ALPHA_PARAM,MAXIMUM_BETA_PARAM,_unObservableData_p);
+		res = lsOpt.optimizeParam(pInDistribution, maxIterations, tol, pWeights, optGammaMixtureLS::ONE_DIM);
+		MDOUBLE resRecompute = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(*_pTree,*_pSc,*_pSp,pWeights,_unObservableData_p);
+		if(!DEQUAL(res,resRecompute)){
+			LOGnOUT(3,<<"--- error: different likelihood after GamMixtureOptimizer::optimizeParam,diff= "<<res-resRecompute <<"\n");
+		}
+		break;
+		}
+	//case TX_CONJUGATE_DERIVATIVES:
+	//	{
+	//	txGamMixtureOptimizer txOpt(_pSp, *_pSc, *_pTree);
+	//	txOpt.setOptimizationParameters(tol, _tolOptSpecific, _tolOptSpecific, _tolOptSpecific);
+	//	res = txOpt.optimizeParam(pInDistribution, maxIterations, pWeights, alg, pOutF);
+	//	break;
+	//	}
+	//case NR_CONJUGATE_DERIVATIVES:
+	//	{
+	//	optGammaMixtureLS opt(_pSp, *_pSc, *_pTree);
+	//	res = opt.optimizeParam(pInDistribution, maxIterations, tol, pWeights, optGammaMixtureLS::CONJUGATE_DERIVATIVES, pOutF);
+	//	break;
+	//	}
+	default:
+		errorMsg::reportError("unknown optimization algorithm in GamMixtureOptimizer::optimizeParam()");
+	}
+	return res;
+}
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GamMixtureOptimizer.h
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GamMixtureOptimizer.h
@ -0,0 +1,52 @@
+#ifndef __GAMMIXTURE_OPTIMIZER
+#define __GAMMIXTURE_OPTIMIZER
+/************************************************************
+GamMixtureOptimizer class is used to find the best Gamma mixture parameters.
+The parameters to otimized are the alpha and beta of each component and the components probabilities.
+The optimizer can choose between several optimization algorithms (EM, ConjugateDerivatives, etc).
+The interface to the optimizer is the functions:
+1. findBestParam() = given a gammaMixture - finds the best parameters.
+2. findBestParamManyStarts() - finds the best parameters but starts from many initial points.
+3. SetOptAlg() - choose the optimization algorithm to be used.   
+************************************************************/
+#include "definitions.h"
+#include "stochasticProcess.h"
+#include "sequenceContainer.h"
+#include "tree.h"
+#include "mixtureDistribution.h"
+#include "unObservableData.h"
+
+
+
+class GamMixtureOptimizer{
+public:
+	enum OptimAlg {EM, ONE_DIM, TX_CONJUGATE_DERIVATIVES, NR_CONJUGATE_DERIVATIVES};
+public:
+
+	explicit GamMixtureOptimizer(stochasticProcess* cur_sp, const sequenceContainer& sc, const tree& inTree, unObservableData* unObservableData_p = NULL);
+	virtual ~GamMixtureOptimizer();
+
+	const stochasticProcess* getSp()  const {return _pSp;}
+	const mixtureDistribution* getMixtureDist()  const {return static_cast<mixtureDistribution*>(_pSp->distr());}
+
+	MDOUBLE findBestParamManyStarts(const Vint pointsNum, const Vint iterNum, const vector<OptimAlg> OptAlgs, const Vdouble tols, const Vdouble * pWeights, ofstream* pOutF = NULL);
+	//return the logLikelihood. the final distribution is stored in the stochasticProcess
+	MDOUBLE findBestParam(const OptimAlg alg, const int maxIterations, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF=NULL);
+
+	void setTolOptSpecific(const MDOUBLE tol) {_tolOptSpecific = tol;}
+
+private:
+	MDOUBLE optimizeParam(mixtureDistribution* pInDistribution, const int maxIterations, const OptimAlg alg, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF);
+
+
+private:	
+	stochasticProcess* _pSp;
+	const sequenceContainer* _pSc;
+	const tree* _pTree;
+	unObservableData* _unObservableData_p;
+
+	MDOUBLE _tolOptSpecific; //tolerance specific to the optimization algorithm
+};
+
+#endif
+
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GamMixtureOptimizer.o
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/GamMixtureOptimizer.o
--- a/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/HIVb.dat.q
+++ b/PTL2/Scripts-DEV/guidance.v2.02/libs/phylogeny/HIVb.dat.q
@ -0,0 +1,24 @@
+""
+"0.16315391	"
+"0.0026528488	0.15680618	"
+"0.77200021	0.0026528488	9.3704985	"
+"0.065662251	0.18661252	0.045663061	0.0026528488	"
+"0.029241185	1.8153444	0.35657046	0.0026528488	0.0026528488	"
+"0.7859595	0.039751241	0.042054709	5.6172481	0.0026528488	1.3583647	"
+"1.1329574	1.9384101	0.17158679	1.5057888	0.47638319	0.032849536	2.0839453	"
+"0.044971782	4.796584	4.0566567	1.0170492	0.12737547	3.7434084	0.063530422	0.0026528488	"
+"0.0026528488	0.35934906	0.3610872	0.0093800488	0.0026528488	0.0026528488	0.0032315889	0.0026528488	0.054707578	"
+"0.11420832	0.37215595	0.0026528488	0.0046480457	0.068855751	0.79296833	0.0026528488	0.0026528488	0.92409864	3.1615537	"
+"0.0026528488	10.850151	4.1938515	0.0026528488	0.0026528488	3.4738365	2.4484839	0.27680089	0.0026528488	0.17101271	0.04324117	"
+"0.009902713	1.3338205	0.0026528488	0.0026528488	0.0026528488	0.1611213	0.093268326	0.0026528488	0.0026528488	5.9458299	2.8224242	0.68043448	"
+"0.0074953058	0.0026528488	0.0026528488	0.0026528488	4.9333171	0.0026528488	0.0026528488	0.15469345	0.077228672	1.803067	4.5230222	0.018180397	0.099760378	"
+"1.1259592	0.68101281	0.0039239772	0.018180397	0.0026528488	2.3727663	0.0063788279	0.0026528488	1.3015831	0.021784823	1.1022958	0.016652568	0.0026528488	0.0026528488	"
+"1.3085601	1.8459052	6.9741802	0.28026286	2.4900381	0.061711098	0.0026528488	2.324113	0.20307398	0.64624988	0.49218621	0.26746605	0.0026528488	0.50747511	2.8532025	"
+"8.4457685	1.5220348	3.6538588	0.14576024	0.39260517	0.12924096	0.15374532	0.19610654	0.37755025	4.5693569	0.023221606	2.4785142	2.6211525	0.0074953058	1.0686577	4.7385556	"
+"0.0026528488	0.52597396	0.0026528488	0.0026528488	1.3968681	0.014142867	0.0026528488	0.64556544	0.036884095	0.0026528488	0.39731344	0.0026528488	0.047262092	0.44002431	0.023584144	0.013196755	0.0026528488	"
+"0.0026528488	0.0052623288	0.93601524	0.35795048	4.0213579	0.059971891	0.042054709	0.0026528488	9.9186301	0.078613459	0.059416384	0.0026528488	0.0026528488	8.13894	0.016149535	0.34382193	0.056055755	0.67924601	"
+"4.0399067	0.043106352	0.014142867	0.55599996	0.22285362	0.011097026	0.54567507	0.50571521	0.0026528488	9.4117238	0.74829436	0.14104083	3.6361006	0.38374731	0.0026528488	0.039751241	0.37629386	0.0026528488	0.021784823	"
+
+
+
+"0.060490222	0.066039665	0.044127815	0.042109048	0.020075899	0.053606488	0.071567447	0.072308239	0.022293943	0.069730629	0.098851122	0.056968211	0.019768318	0.028809447	0.046025282	0.05060433	0.053636813	0.033011601	0.028350243	0.061625237	"
--- a/Show More
+++ b/Show More
				`@ -0,0 +1 @@`
				((seq0017:0.159520,((((seq0029:0.000335,seq0030:0.000001):0.298687,((seq0026:0.118374,((seq0022:0.000001,(seq0021:0.000001,(seq0020:0.000001,(seq0023:0.000001,seq0024:0.000001):0.003307):0.001691):0.000865):0.194370,(seq0019:0.213074,(seq0047:0.000001,(seq0040:0.218288,seq0060:0.741067):0.558436):0.264600):0.089062):0.026603):0.078072,(((seq0059:0.416185,(((seq0051:0.002343,seq0052:0.051365):0.156768,(seq0050:0.102723,(seq0048:0.000001,seq0049:0.000606):0.156109):0.026679):0.088477,(seq0046:0.251155,(((seq0055:0.122540,(seq0053:0.000001,seq0054:0.050064):0.060836):0.112993,(seq0058:0.094203,(seq0056:0.146811,seq0057:0.074128):0.032205):0.099845):0.238408,(seq0045:0.176854,(seq0044:0.062128,(seq0041:0.000001,(seq0042:0.014202,seq0043:0.000001):0.007922):0.069848):0.072547):0.053735):0.020337):0.040887):0.078664):0.063075,((seq0039:0.164075,(seq0037:0.088700,seq0038:0.060206):0.105530):0.093641,((seq0000:0.095561,seq0001:0.071802):0.371565,(seq0061:0.262548,(seq0062:0.274390,(seq0025:0.000001,seq0063:0.456008):0.072702):0.040402):0.114369):0.042115):0.053357):0.040190,(seq0027:0.279481,seq0028:0.236863):0.026728):0.009003):0.005029):0.027732,(seq0018:0.176464,((seq0035:0.000001,seq0036:0.000001):0.279842,((seq0033:0.064803,seq0034:0.034665):0.126784,(seq0031:0.000001,seq0032:0.021257):0.110018):0.058727):0.055398):0.008537):0.026864,(seq0015:0.079754,seq0016:0.205938):0.020846):0.015120):0.020439,((seq0009:0.022972,seq0010:0.000001):0.164226,(seq0014:0.189401,(seq0011:0.000001,(seq0012:0.012592,seq0013:0.000001):0.003812):0.062063):0.019146):0.014995,(seq0008:0.161694,((seq0007:0.000001,(seq0005:0.000001,seq0006:0.000001):0.002884):0.117868,(seq0002:0.000001,(seq0003:0.002943,seq0004:0.003582):0.007856):0.097737):0.007560):0.006500);