mrBayesTreeFromMixedMSA: 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 mixed multiple sequence alignment, e.g. CDS 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 mixed multiple sequence alignment, e.g. CDS AND an alignment of additional e.g. morphological data.

Usage

mrBayesTreeFromMixedMSA(msa.lst, msa.types, mr.bayes.dir, gene.group.name,
  mr.bayes.n.chains = getOption("mc.cores", 4))

Arguments

msa.lst	A list of multiple sequence alignments, a mix of DNA and Standard data
msa.types	a character vector of the types of each MSA: DNA, Codon, or Standard
mr.bayes.dir	The file directory in which to store the output file
the	name of the analysis. Will be the head of the file name holding the input for Mr Bayes

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