LikelihoodFreePhylogenetics

Options

./LFP
version 1.0
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-m < stats | show | CodonMutSelFiniteABC | CodonMutSelSBDPABC | CodonDegMutSelFiniteABC | CodonDegMutSelSBDPABC | CodonMutSelFinite | CodonMutSelSBDP | CodonMutSelFinitePPred | CodonMutSelSBDPPPred >
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#SUMMARIES
#ANCSUMMARIES
#ACCSUMMARIES
#PARAM
#SSMAP
#MAP
#ANCESTRALMAP
#DIST
#TRANS
#SPEUDODATA
#NRUN
#SAMPLING
#LOCALPARAM
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Running rejection sampling

./LFP -m CodonMutSelSBDPABC ACO1-2673-MSAAGTRW-A-GTRWCpG.conf

Configuration file:

#SUMMARIES pwAC pwAG pwAT pwCG pwCT pwGT dinuc31CG dinuc31TG dinuc31CA nuc3A nuc3C nuc3G nuc3T pwAA
#PARAM chainID root lambda_CpG lambda_TBL lambda_omega nucsA nucsC nucsG nucsT nucrrAC nucrrAG nucrrAT nucrrCG nucrrCT nucrrGT
#MAP gtnrAC gtnrAG gtnrAT gtnrCA gtnrCG gtnrCT gtnrGA gtnrGC gtnrGT gtnrTA gtnrTC gtnrTG dinuc31CGTG dinuc31CGCA Nsub Nsynsub
#SAMPLING 600 4 999
#NRUN 1000000 10000
#NTHREADS 6
#OUTPUT /ABC/ACO1-2673-MSAAGTRW-A-GTRWCpG
#LOCALPARAM -d ACO1.puz -chain /step_1/ACO1-2673-MSAAGTRW-A -code Universal -iscodon -freeroot Echinops Procavia -freelambdaTBL -freelambdaCpG -freegtr -freelambdaomega -rootlength 10 -priorlambdaomega log2Unif -priorlambdaCpG log10Unif -priorlambdaTBL log2Unif

Simulating from M[GTR+λCpG]-[1CatAA] or M[GTR+λCpG]-[1CatCodon]

./LFP -m CodonMutSelFinite ANKRD28-M0GTRW-A-M0GTRWCpG.conf

Configuration file: ANKRD28-M0GTRW-A-M0GTRWCpG.conf

#SUMMARIES A C D E F G H I K L M N P Q R S T V W Y
#PARAM chainID root lambda_CpG lambda_TBL lambda_omega nucsA nucsC nucsG nucsT nucrrAC nucrrAG nucrrAT nucrrCG nucrrCT nucrrGT
#MAP gtnrAC gtnrAG gtnrAT gtnrCA gtnrCG gtnrCT gtnrGA gtnrGC gtnrGT gtnrTA gtnrTC gtnrTG dinuc12CGTG dinuc12CGCA dinuc23CGTG dinuc23CGCA dinuc31CGTG dinuc31CGCA Nsub Nsynsub
#NRUN 10 1000
#NTHREADS 1
#OUTPUT /ppred/ANKRD28-M0GTRW-A-LFP-M0GTRWCpG
#LOCALPARAM -d ANKRD28.puz -chain ANKRD28-M0GTRW-A -iscodon -code Universal -start 600 -every 4 -until 1000 -fixroot Echinops Procavia 0.9 -lambdaCpG 1.0 -lambdaTBL 1.0 -lambdaOmega 1.0 -tophylip -rootlength 10

Where λCpG is a multiplicative parameter that modulate the transition rate of CpG context
Where λTBL is a multiplicative parameter that modulate the all the branch lengths
Where λomega \ λomega* is a multiplicative parameter that modulate Omega or Omega*