|-s [MSA file]||
The input sequence file name.
The following formats are supported: Mase, Molphy, Phylip, Clustal, Fasta
|-o [output Directory]||
The results output directory. Result files include: |
mcRate4Site.txt – The final rate estimates over all chains.
For each chain, numbered XX below, 4 result files are created:
chainXXr4s.txt – the rate estimates for this chain only.
chainXX_log.txt – the acceptance rate for each proposal mechanism.
chainXX_trees.txt – a list of all trees sampled.
chainXX_res.txt – the likelihood and alpha parameter for each sampled point.
|-a [sequence name]||Reference sequence name in the MSA. The conservation scores are printed based on the amino-acids in this sequence.||First sequence in the MSA|
|-n [chains number]||Number of independent MCMC chains to run.||1|
|-k [categories number]||The number of discrete Gamma categories||16|
|-m [evolutionary model]||
The following amino-acids models are supported:|
DAY (-md), JTT (-mj), REV (-mr), aaJC (-ma).
For nucleotides, currently only the JC model is supported (-mn)
|-e [thinning rounds]||-eXX; Chain will be sampled every XXth step.||10|
|-b [burnin time]||-bXX; The chain will not sample during the first XX steps.||10,000|
|-i [inference time]||-iXX; The chain will run for at most XX steps.||100,000|
|-g||Remove positions with gaps.||Off|
|-f||Homogenous rate model. Default is Gamma.||Off|