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194 lines
12 KiB
Plaintext
194 lines
12 KiB
Plaintext
# $RCSfile$ $Revision: 1932 $ $Date: 2007-04-10 12:05:04 +0300 (Tue, 10 Apr 2007) $
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purpose "structural EM based Phylogeny"
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package "semphy"
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version "1.0.b1"
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section "Algorithm Options"
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# algorithm options
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section "Which algorithm to run"
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#defgroup "Run Options" groupdesc="Which algorithm to run"
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option "SEMPHY" S "Do SEMPHY step" flag off
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option "bbl" n "Only optimize branch length" flag off
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option "likelihood" L "Compute likelihood for fixed tree" flag off
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option "PerPosLike" P "Compute likelihood per position for a fixed tree" flag off
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option "PerPosPosterior" B "Compute likelihood per position and Bayesian posterior" flag off
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#option "NJ" J "compute NJ tree only" flag off
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option "rate" R "optimize rate of gene" flag off
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#section "Other Algorithm Options"
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#option "exact" e "Compute exact counts" flag off
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#option "maxDistance" x "'infinity' distance for sequence pairs" float default="2.0" no
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section "Advanced Algorithm Options"
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#option "dont-use-NJ" N "Do not Use NJ to break stars in treeRearrange" flag hidden on
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option "max-semphy-iter" M "Max number of SEM iterations" int default="100" hidden no
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option "epsilonLikelihoodImprovement4iterNJ" - "The threshold for optimization of likelihood of the tree, in iterative distance-based tree reconstruction" float default="0.01" hidden no
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option "epsilonLikelihoodImprovement4pairwiseDistance" - "The threshold for optimization of likelihood of a pair of sequences, in pairwise distance optimization" float default="0.0001" hidden no
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option "epsilonLikelihoodImprovement4alphaOptimiz" - "The threshold for optimization of likelihood of the tree, in alpha optimization (also used for Nu optimization when using --ssrv)" float default="0.01" hidden no
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option "epsilonLikelihoodImprovement4BBL" - "The threshold for optimization of likelihood of the tree, in branch-lengths optimization" float default="0.01" hidden no
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#option "ADVBBLEpsilinLikeToll" - "BBL and BBL LL tol" float default="0.05" hidden no
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option "maxNumOfBBLIter" - "Number of BBL iterations in BBL+ALPHA optimization" int default="10" hidden no
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#option "ADVNoPost" - "do not use posterior" flag hidden off
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option "consurf" - "version for use in consurf" flag hidden off
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defgroup "DistanceTableEstimationMethod" groupdesc="Method used for computing the distance table for the initial tree NJ construction"
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section "Non Iterative methods"
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#section "XXXXXX Pairwise distance estimation methods"
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groupoption "NJ" J "'classic' Neighbor Joining (same as homogeneousRates)" group="DistanceTableEstimationMethod"
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groupoption "homogeneousRatesDTME" - "homogeneous rates MLE distance" group="DistanceTableEstimationMethod"
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groupoption "pairwiseGammaDTME" - "Gamma-ASRV with alpha optimized for each pair. (must give either --alpha or --optimizeAlpha)" group="DistanceTableEstimationMethod"
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section "Iterative distance-based tree reconstruction, with distance estimation methods that utilize side information from the tree of the previous iteration"
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groupoption "commonAlphaDTME" - "Side information is the alpha parameter.(must use --optimizeAlpha; may give an initial alpha value in --alpha)" group="DistanceTableEstimationMethod"
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groupoption "rate4siteDTME" - "Side information is the ML rate for each site" group="DistanceTableEstimationMethod"
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groupoption "posteriorDTME" - "Side information is the posterior probabilities of the rates at each site. (must use --optimizeAlpha; may give an initial alpha value in --alpha)" group="DistanceTableEstimationMethod"
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# we need to change the iterative common-alpha (and the pairwise) to use exact gamma (using cmdline2ExactGammaStochasticProcess, which uses alphaTrivialAccelerator)
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#groupoption "asrvExactGammaDTME" - "Exact Gamma-ASRV, given alpha (must give alpha parameter)" group="DistanceTableEstimationMethod"
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section "Bootstrap"
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option "BPrepeats" - "Use bootstrap and set number of repeats" int no
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#option "BPfile" - "Use bootstrap and read the weights from a file" string typestr="FILENAME" no
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option "BPconsensus" - "Use bootstrap and compute a Consensus tree" int no
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option "BPonUserTree" - "Use compute support for user provided tree" flag off
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#option "paramFile" f "Parameter file name" string no
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#option "cin" I "Get input sequence file from cin" flag off
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# annealing:
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#option "anneal" A "Do anneal step" flag off
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#option "ratchet" R "Do Ratchet step" flag off
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#option "start-temp" H "Starting temp" float no
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#option "cooling-factor" c "Variance decay factor for anneal noise" float default="1.1" no
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#option "final-temp" C "Final temperature of anneal noise" float default="0.1" no
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#option "adversarial" - "Use Adversarial Re-weighting" flag off
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#option "learning-rate" L "learning rate for Adversary" float default="1.0" no
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#option "Orig-dumping" D "Dumping to the original weights" float default="0.5" no
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#option "prev-dumping" X "Dumping to the previous weights" float default="0.5" no
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# $Id: evolObjs.args 5928 2009-02-25 16:30:50Z privmane $
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#purpose "structural EM based Phylogeny"
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#package "semphy"
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#version "1.0.b2"
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#files
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section "Basic Options"
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option "sequence" s "Sequence file name" string typestr="FILENAME" default="-" no
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option "tree" t "Tree file name" string typestr="FILENAME" no
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option "constraint" c "Constraint Tree file name" string typestr="FILENAME" no
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option "outputfile" o "Output file" string typestr="FILENAME" default="-" no
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option "treeoutputfile" T "Tree output file" string typestr="FILENAME" default="-" no
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option "gaps" g "Remove positions with gaps" flag off
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option "seed" r "Seed random number generator" long no
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# model options:
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section "Model Options"
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option "alphabet" a "Alphabet Size" int typestr="4|20|61|64" default="20" no
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option "ratio" z "Transition/Transversion ratio" float default="2.0" no
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option "ACGprob" p "User input nucleotide frequencies. String separated list for A,C,G" string typestr="A,C,G" default="0.25,0.25,0.25" no
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option "inputRate" - "Set External globalRate" float default="1.0" no
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section "Among Site Rate Variation (ASRV)"
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option "homogeneous" H "Don't use Gamma ASRV" flag off
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option "alpha" A "Set alpha for Gamma ASRV" float typestr="Alpha" no
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option "optimizeAlpha" O "Optimize alpha for Gamma ASRV" flag off
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option "categories" C "Number of categories to use with descrete Gamma ASRV" int default="8" no
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option "laguerre" - "Use Laguerre approximation of Gamma - CURRENTLY NOT IMPLIMENTED" flag off
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option "ssrv" - "Use a Site-Specific Rate Variation model (SSRV)" flag off
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option "nu" - "Set Nu for the SSRV model" float typestr="Nu" default="1.0" no
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option "posteriorRates" - "File with posterior distribution of the rate for each sequence site - for ASRV" string typestr="FILENAME" no
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defgroup "Model" groupdesc="Model type"
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groupoption "day" - "Use 'day' model" group="Model"
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groupoption "jtt" - "Use 'jtt' model (default)" group="Model"
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groupoption "rev" - "Use 'rev' model" group="Model"
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groupoption "wag" - "Use 'wag' model" group="Model"
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groupoption "cprev" - "Use 'cprev' model" group="Model"
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groupoption "nucjc" - "Use nucleic acid JC model" group="Model"
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groupoption "aaJC" - "Use amino acid JC model" group="Model"
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groupoption "k2p" - "Use 'k2p' model" group="Model"
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groupoption "hky" - "Use 'hky' model" group="Model"
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groupoption "tamura92" - "Use 'tamura92' model" group="Model"
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groupoption "gtr" - "Use 'gtr' model (general reversible model)" group="Model"
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option "modelfile" - "Read replacement matrix from user input file" string typestr="NAME" no
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section "Log Options"
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option "verbose" v "Log report level (verbose)" int default="1" no
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option "Logfile" l "Log output file name" string typestr="FILENAME" default="-" no
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## not for general ggo? ##
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## not for general ggo? ## section "Algorithm Options"
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## not for general ggo? ##
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## not for general ggo? ## # algorithm options
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## not for general ggo? ## section "Which algorithm to run"
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## not for general ggo? ## #defgroup "Run Options" groupdesc="Which algorithm to run"
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## not for general ggo? ##
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## not for general ggo? ## option "SEMPHY" S "Do SEMPHY step" flag off
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## not for general ggo? ## option "bbl" n "Only optimize branch length" flag off
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## not for general ggo? ## option "likelihood" L "Compute likelihood for fixed tree" flag off
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## not for general ggo? ## option "PerPosLike" P "Compute likelihood per position for a fixed tree" flag off
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## not for general ggo? ## option "NJ" J "compute NJ tree only" flag off
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## not for general ggo? ##
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## not for general ggo? ## option "rate" R "optimize rate of gene" flag off
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## not for general ggo? ##
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## not for general ggo? ##
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## not for general ggo? ## section "Other Algorithm Options"
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## not for general ggo? ## option "max-semphy-iter" M "Max number of SEM iterations" int default="100" no
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## not for general ggo? ## option "max-bbl-iter" b "Max number of BBL iterations" int default="1000" no
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## not for general ggo? ## #option "min-improv" d "Minimum improvement" float default="0.001" no
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## not for general ggo? ## option "gaps" g "Remove positions with gaps" flag off
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## not for general ggo? ## option "dont-use-NJ" N "Do not Use NJ to break stars in treeRearrange" flag on
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## not for general ggo? ## #option "exact" e "Compute exact counts" flag off
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## not for general ggo? ## #option "maxDistance" x "'infinity' distance for sequence pairs" float default="2.0" no
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## not for general ggo? ##
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## not for general ggo ## section "Bootstrap"
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## not for general ggo ## option "BPrepeats" - "Use bootstrap and set number of repeats" int no
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## not for general ggo ## option "BPfile" - "Use bootstrap and read the weights from a file" string typestr="FILENAME" no
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## not for general ggo ## option "BPconsensus" - "Use bootstrap and compute a Consensus tree" int no
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## not for general ggo ## option "BPonUserTree" - "Use compute support for user provided tree" flag off
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## not for general ggo ##
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## not for general ggo ##
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## not for general ggo ## section "Advanced @@"
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## not for general ggo ## option "ADVBBLEpsilinLikeToll" - "@@ BBL and BBL LL tol" float default="0.05" no
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## not for general ggo ## option "ADVNumOfBBLIterInBBLPlusAlpha" - "@@ Numver of BBL interations in BBL+ALPHA" int default="10" no
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## not for general ggo ## option "ADVNoPost" - "@@ do not use posterior" flag off
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## not for general ggo ## option "consurf" - "@@ version for consurf use" flag off
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## not for general ggo ## option "numbins" - "@@ number of bins in gamma" int default="4" no
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## not for general ggo ##
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## not for general ggo ##
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## not for general ggo ## #option "paramFile" f "Parameter file name" string no
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## not for general ggo ## #option "cin" I "Get input sequence file from cin" flag off
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## not for general ggo ##
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## not for general ggo ## # annealing:
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## not for general ggo ## #option "anneal" A "Do anneal step" flag off
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## not for general ggo ## #option "ratchet" R "Do Ratchet step" flag off
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## not for general ggo ## #option "start-temp" H "Starting temp" float no
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## not for general ggo ## #option "cooling-factor" c "Variance decay factor for anneal noise" float default="1.1" no
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## not for general ggo ## #option "final-temp" C "Final temperature of anneal noise" float default="0.1" no
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## not for general ggo ## #option "adversarial" - "Use Adversarial Re-weighting" flag off
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## not for general ggo ## #option "learning-rate" L "learning rate for Adversary" float default="1.0" no
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## not for general ggo ## #option "Orig-dumping" D "Dumping to the original weights" float default="0.5" no
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## not for general ggo ## #option "prev-dumping" X "Dumping to the previous weights" float default="0.5" no
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## not for general ggo ##
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