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81 lines
5.1 KiB
Plaintext
81 lines
5.1 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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