mrBayesProteinTreeFromMixedMSA: Generates a valid input file for Mr Bayes, which will...

In asishallab/GeneFamilies: Analyses different properties of gene families

Generates a valid input file for Mr Bayes, which will generate a Bayesian phylogeny from a multiple amino acid sequence alignment AND an alignment of additional e.g. morphological data.

Description

Generates a valid input file for Mr Bayes, which will generate a Bayesian phylogeny from a multiple amino acid sequence alignment AND an alignment of additional e.g. morphological data.

Usage

mrBayesProteinTreeFromMixedMSA(aa.msa, extra.msa, mr.bayes.dir,
  gene.group.name, mr.bayes.n.chains = getOption("mc.cores", 4))

Arguments

aa.msa	an instance of Biostrings::AAStringSet representing the MSA
extra.msa	a mamed list of additional e.g. morphological data, aligned. Names have to be identical with names of 'aa.msa'.
mr.bayes.dir	a valid file path to the output directory in which to store the Mr Bayes analysis related files
gene.group.name	the name of the group of proteins to generate the Bayesian tree for
mr.bayes.n.chains	number of chains to use in Mr. Bayes, default is 'mc.cores' or 4, if 'mc.cores' is not set.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.