geneTreeFilter: Utility for filtering genetrees based on ingroup monophyly or...

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Utility for filtering genetrees based on ingroup monophyly or coverage

Description

Utility for filtering genetrees based on ingroup monophyly or coverage

Usage

geneTreeFilter(
ingroup=ingroupTaxa, 
outgroup=outgroupTaxa, 
threshold=1, 
tree_file_dir="path/to/files", 
tree_file_ext=".tre"
)

Arguments

ingroup	input vector of ingroups
outgroup	input vector of vector of outgroups
threshold	the minimum number of ingroup sequences, defaults to 1
tree_file_dir	string of the directory path for tree files
tree_file_ext	string extension of tree files defaults to ".contree"

Value

This function uses a user supplied vector of a target ingroup and outgroup taxa along with a path to a directory containing newick format genetrees and their extension (e.g. ".tre", ".contree", etc) to assess sufficient taxon coverage within a specific ingroup using a user defined threshold, and whether the ingroup of interest is resolved as monophyletic. The function returns a dataframe that gives each genetree name, the number of ingroup taxa present, and whether these pass inspection. Trees that do not pass due to low coverage, lack of outgroups, or non-monophyly are indicated by the term "omit".

Author(s)

Derrek Pope, [e-mail]

Examples

ingroupTaxa<-c("TaxonA", "TaxonB", "TaxonC", "TaxonD", "TaxonE")
outgroupTaxa<-c("TaxonZ", "TaxonY", "TaxonX")
geneTreeFilter(ingroup=ingroupTaxa, outgroup=outgroupTaxa, threshold=1, tree_file_dir="path/to/files", tree_file_ext=".tre")

carolinafishes/toast documentation built on Dec. 19, 2024, 12:47 a.m.