astralRunner: astralRunner

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

astralRunner

Description

This function runs many astral analyses across a folder of concatenated gene trees

Usage

astralRunner(
  concat.genetree.folder = NULL,
  output.dir = NULL,
  overwrite = FALSE,
  astral.path = NULL,
  astral.t = 2,
  quiet = TRUE,
  multi.thread = TRUE,
  memory = "1g"
)

Arguments

concat.genetree.folder	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
astral.path	the absolute file path to the ASTRAL-III jar file
astral.t	the ASTRAL-III "t" parameter for different annotations, t = 2 is all annotation
quiet	TRUE hides the screen output from astral
multi.thread	TRUE to use Astral-MP multithreading
memory	memory value to be passed to java. Should be in "Xg" format, X = an integer

Value

Astral is run using this function as a wrapper. The astral output is saved to file, and can optionally be read into R as an ape phylo object using load.tree = TRUE.

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