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163 lines
6.9 KiB
HTML
163 lines
6.9 KiB
HTML
<html>
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<head>
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<META NAME="date" CONTENT="2009-12-31">
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<META NAME="author" CONTENT="Osnat Penn,Eyal Privman,Haim Ashkenazy,Giddy Landan,Dan Graur,Tal Pupko">
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<META NAME="keywords" CONTENT="Multiple sequence alignment, guide tree, alignment confidence,Guidance server">
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<META NAME="description" CONTENT="GUIDANCE: a web server for assessing alignment confidence score">
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<meta http-equiv="X-UA-Compatible" content="IE=EmulateIE7">
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<title>GUIDANCE SOURCE CODE</title>
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<link rel="stylesheet" type="text/css" href="guidance.css" />
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</head>
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<body onLoad="init()" bgcolor="#F2F2F2" align=left marginheight=0 marginwidth=0 topmargin=0 leftmargin=0 rightmargin=0>
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<table cols=2 cellspacing=0 cellpadding=10 width=750 border=0>
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<tr align=left>
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<td width=125 ALIGN= center VALIGN=top bgcolor="#99CCFF">
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<script language="javascript" src="title.js"> </script>
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</td>
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<td width=825 ALIGN=left VALIGN=top>
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<h1 align=center><font face="Comic Sans MS" size="6" COLOR="#003399">
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Source Code</font> <br>
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</h1>
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<font face=Verdana size=2>
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<br><b>
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Please note that the GUIDANCE source code is freely distributed for academic use only (see <a href="source.html#copyrights">copyrights</a> statement below)</b><br><br>
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</font>
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<br>
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1. <a href="source.html#download">Downloading and compiling GUIDANCE.</a><br>
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2. <a href="source.html#run">Running GUIDANCE<br></a><br>
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<a NAME=download><font face=Verdana size=4><b><u>Downloading and Compiling GUIDANCE</u></b></font></a><br>
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The following instructions should work right out of the box for
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UNIX-like systems. Mac should also work in principle, but is not yet
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supported. Windows will require some additional work, such as setting
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up a cygwin environment.<br>
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<br>
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1. Download the <a href="guidance.v1.01.tgz">GUIDANCE source code</a>. <br>
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2. Unzip and untar the files:<br>
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<p>
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<blockquote>
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tar -xzvf guidance.v1.01.tgz
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</blockquote>
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</p>
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This will create a directory named guidance.v1.01<br>
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<br>
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3. Make: <br>
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<p>
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<blockquote>
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cd guidance.v1.01<br>
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make
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</blockquote>
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</p>
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4. Check if you have the desired alignment program(s) installed:<br>
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<ul>
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<li><b>MAFFT:</b> Type "mafft" and check that you have version 6.712 or newer.</li>
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<ul><li>Else download and install MAFFT from:<br>
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<a href="http://mafft.cbrc.jp/alignment/software/">http://mafft.cbrc.jp/alignment/software/</a></li></ul>
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<li><b>PRANK:</b> Type "prank" and check that you have version v.100223 or newer.</li>
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<ul><LI>Else download and install PRANK from:<br>
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<a href="http://www.ebi.ac.uk/goldman-srv/prank/prank/">http://www.ebi.ac.uk/goldman-srv/prank/prank/</a></li></ul>
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<li><B>CLUSTALW:</B> Type "clustalw" and check that you have it insalled<br>
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<ul><li>Else download and install CLUSTALW from:<br>
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<a href="http://www.ebi.ac.uk/Tools/clustalw2/index.html">http://www.ebi.ac.uk/Tools/clustalw2/index.html</a></li></ul><br>
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</ul>
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5. GUIDANCE also uses Perl and BioPerl:
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<ul>
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<li>Type "perl -v" and check that you Perl installed.</li>
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<ul><li>Else download and install it from:<br>
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<a href="http://www.perl.org/">http://www.perl.org/</a></li></ul>
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<li>Type "perl -e 'use Bio::SeqIO'" to check that you have BioPerl.</li>
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<ul><li>Else download and install it from:<br>
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<a href="http://www.bioperl.org/">http://www.bioperl.org/</a></li></ul>
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</ul>
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<br>
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<b>For any problems - please <a
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href=mailto:bioSequence@tauex.tau.ac.il>contact us</a><br><br></b>
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<a NAME=run><font face=Verdana size=4><b><u>Running GUIDANCE</u></b></font></a><br>
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Run the Perl script: guidance/www/Guidance/run_calc.pl<br>
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(Note that you cannot move this script out of its directory, because it
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uses relative paths to other files in other directories. Sorry)<br>
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GUIDANCE uses flags in the command line arguments: (for help, type:
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"guidance")<br>
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<br>
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<b>USAGE:</b> guidance --seqFile SEQFILE --msaProgram
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[MAFFT|PRANK|CLUSTALW] --seqType [aa|nuc|codon] --outDir OUTDIR<br>
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<br>
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<b>Required parameters:</b><br>
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<b>--seqFile:</b> Input sequence file in FASTA format<br>
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<b>--msaProgram:</b> Which MSA program to use<br>
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<b>--seqType:</b> Type of sequences for alignment (amino acids,
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nucleotides, or codons)<br>
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<b>--outDir:</b> Output directory that will be created automatically
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and hold all output files<br>
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<br>
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<b>Optional parameters:</b><br>
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<b>--program</b> [GUIDANCE|HoT] Default=GUIDANCE<br>
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<b>--bootstraps:</b> Number of bootstrap iterations (only for
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GUIDQANCE). Defaut=100<br>
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<b>--genCode:</b> Genetic code identifier (only for codon
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sequences). Default=1<br>
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1) Nuclear Standard<br>
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15) Nuclear Blepharisma<br>
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6) Nuclear Ciliate<br>
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10) Nuclear Euplotid<br>
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2) Mitochondria Vertebrate<br>
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5) Mitochondria Invertebrate<br>
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3) Mitochondria Yeast<br>
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13) Mitochondria Ascidian<br>
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9) Mitochondria Echinoderm<br>
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14) Mitochondria Flatworm<br>
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4) Mitochondria Protozoan<br>
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<b>--outOrder</b> [aligned|as_input] default=aligned<br>
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<b>--msaFile:</b> Input alignment file - not recommended, see
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the <a href="http://guidance.tau.ac.il/overview.html#InputMSA">overview</a> section<br>
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<b>--seqCutoff:</b> Confidence cutoff between 0 to 1. Default=0.6<br>
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<b>--colCutoff:</b> Confidence cutoff between 0 to 1. Default=0.93<br>
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<b>--mafft:</b> path to mafft executable. Default=mafft<br>
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<b>--prank:</b> path to prank executable. Default=prank<br>
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<br>
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<font face="Verdana" size="3" color="red"><u><b>EXAMPLES:</b></u></font>
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<ul>
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<li><b>guidance --seqFile protein.fas --msaProgram MAFFT --seqType aa --outDir protein.guidance</b><br>
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- will align the amino acid sequences in the fasta file "protein.fas" using MAFFT and output all results to the diretory "protein.guidance" </li>
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<br>
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<li><b>guidance --seqFile codingSeq.fas --msaProgram PRANK --seqType codon --outDir codingSeq.guidance --genCode 2 --bootstraps 30</b><br>
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- 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 "codingSeq.guidance". Only 30 bootstrap iterations will be done instead of the default 100 (cut run-time by a factor of 3) </li>
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<br>
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</ul>
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<br>
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<center>
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<font face="Comic Sans MS" COLOR="#91219E">For any problems or questions
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please contact us at <a href=mailto:bioSequence@tauex.tau.ac.il>
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bioSequence@tauex.tau.ac.il.</a><br>Enjoy!</font><br><br></center>
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</font>
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<hr>
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<a NAME=copyrights><font face=Verdana size="4" color='red'><b><u>Copyrights:</u></b></font></a><br>
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<ul>
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<font face=Verdana size=2>
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<li><b>To modify the code, or use parts of it for other purposes,
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permission should be requested. Please contact <a
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href=mailto:talp@post.tau.ac.il>Tal Pupko</a><br></b>
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<br></li>
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<li><b>Please note that the use of the GUIDANCE program is for academic
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use only<br></b>
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</font></li>
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</ul></FONT>
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<hr><br><br>
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</table>
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</body>
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</html>
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