concordanceFactors: concordanceFactors

In chutter/AstralPlane: R Package For Preparing, Running, Analyzing and Plotting for the Species Tree Program ASTRAL-III

concordanceFactors

Description

This function runs concordance factor analyses using IQTREE2

Usage

concordanceFactors(
  species.tree = NULL,
  alignment = NULL,
  gene.trees = NULL,
  output.name = NULL,
  overwrite = FALSE,
  quiet = TRUE,
  threads = 1
)

Arguments

species.tree	a species trees (e.g. from astral) to assess concordance
alignment	a concatenated alignment file
gene.trees	a folder of genetree files that are concatenated.
output.name	the output name for the concordance files
overwrite	overwrite = TRUE to overwrite existing files
quiet	hides the screen output from astral if desired
threads	how many threads to use

Value

IQ-TREE 2 concordance factors files

Examples

concordanceFactors(species.tree = paste0(species.tree.dir, "/", a.files[i]),
                   alignment = paste0(alignment.dir, "/", align.file),
                   gene.trees = paste0(genetree.dir, "/", gene.tree),
                   output.name = paste0(output.dir, "/", dataset.name),
                   quiet = quiet, threads = threads)

chutter/AstralPlane documentation built on Aug. 29, 2024, 5:21 p.m.