buildPhylogeneticTree: Uses FastTree[MP] to generate a maximum likelihood tree based...

In asishallab/GeneFamilies: Analyses different properties of gene families

Uses FastTree[MP] to generate a maximum likelihood tree based on sequence profiles.

Description

Uses FastTree[MP] to generate a maximum likelihood tree based on sequence profiles.

Usage

buildPhylogeneticTree(path.2.cds.msa, path.2.ml.tree,
  fast.tree.call = getOption("fast.tree.call", paste("OMP_NUM_THREADS=",
  getOption("mc.cores", 1), " FastTreeMP -nt -gtr -gamma", sep = "")))

Arguments

'path.2.cds.msa'	a valid file path to the codon multiple sequence alignment to feed into FastTree[MP]
'path.2.ml.tree'	a valid file path in which to store the resulting tree in newick format
'fast.tree.call'	the command whith which to invoke FastTree[MP]

Value

TRUE if and only if no error occurred.

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