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84 lines
3.9 KiB
Plaintext
84 lines
3.9 KiB
Plaintext
# $Id: cmdline.ggo 962 2006-11-07 15:13:34Z privmane $
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purpose "structural EM based Phylogeny"
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package "semphy"
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version "1.0.a3"
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# test default values
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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 "format" f "Sequence format: [phylip], clustal, molphy, mase, fasta" string default="phylip" 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 tree file" string typestr="FILENAME" default="-" 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"default="20" no
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option "ratio" z "Transition/Transversion ratio" float default="2" 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 "gamma" G "Use Gamma RVAS (4 bins) and set alpha" float default="0.3" no
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option "optimizeGamma" O "Optimize Gamma and use it" flag off
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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 'k2p' model" group="Model"
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option "modelfile" - "Use user input file as model" 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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section "Algorithm Options"
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# algorithm options
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defgroup "Run Options" groupdesc="Which algorithm to run"
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groupoption "SEMPHY" S "Do SEMPHY step (default)" group="Run Options"
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groupoption "bbl" n "Only optimize branch length" group="Run Options"
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groupoption "likelihood" L "Compute likelihood for fixed tree" group="Run Options"
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groupoption "NJ" J "compute NJ tree only" group="Run Options"
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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 "max-semphy-iter" M "Max number of SEM iterations" int default="100" no
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option "max-bbl-iter" b "Max number of BBL iterations" int default="1000" no
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option "min-improv" d "Minimum improvement" float default="0.001" no
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option "gaps" g "Remove positions with gaps" flag off
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option "dont-use-NJ" N "Do not Use NJ to break stars in treeRearrange" flag on
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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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option "seed" r "Seed random number generator" long no
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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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