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

View source: R/selection_funks.R

mrBayesCdsTreeR Documentation

Generates a valid input file for Mr Bayes, which will generate a Bayesian phylogeny from a multiple coding sequence (codons) alignment.

Description

Generates a valid input file for Mr Bayes, which will generate a Bayesian phylogeny from a multiple coding sequence (codons) alignment.

Usage

mrBayesCdsTree(cds.msa, mr.bayes.dir, gene.group.name,
  mr.bayes.n.chains = getOption("mc.cores", 4))

Arguments

cds.msa

an instance of Biostrings::DNAStringSet representing the MSA of coding sequences (CODONS)

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.