concordanceRunner: concordanceRunner

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

concordanceRunner

Description

This function runs many concordance factor analyses using IQTREE2

Usage

concordanceRunner(
  alignment.dir = NULL,
  species.tree.dir = NULL,
  genetree.dir = NULL,
  output.dir = "concordance-factors",
  overwrite = FALSE,
  quiet = TRUE,
  threads = 1
)

Arguments

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

Value

IQTree concordance factors are run using this function as a wrapper. The CF output is saved to file, and can be read into R using the function "readConcordance".

Examples

paths
genetree.path = paste0(work.dir, "/filtered-genetrees-concatenated")
alignment.path = paste0(work.dir, "/filtered-alignments-concatenated")
output.path = "concordance-factors"
astral.tree.path = paste0(work.dir, "/", astral.dir)

concordanceRunner(alignment.dir = alignment.path,
                 species.tree.dir = astral.tree.path,
                 genetree.dir = genetree.path,
                 output.dir = "concordance-factors",
                 overwrite = TRUE,
                 quiet = TRUE,
                 threads  = 6)

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