runAstral: runAstral

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

runAstral

Description

This function sets up an astral run from gene trees

Usage

runAstral(
  input.genetrees = NULL,
  output.name = NULL,
  astral.path = NULL,
  astral.t = 2,
  quiet = TRUE,
  load.tree = FALSE,
  overwrite = FALSE,
  multi.thread = TRUE,
  memory = "1g"
)

Arguments

input.genetrees	a file of genetrees from setupAstral
output.name	the save name for the astral file
astral.path	the absolute path to astral. Needed because astral needs it.
astral.t	the t value from astral for different annotations. t = 2, all annotations is recommended for full functionality
quiet	hides the screen output from astral if desired
load.tree	should the tree be loaded into R?
overwrite	whether to overwrite an existing dataset
multi.thread	whether to use Astral-MP multithreading or not.
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.

Examples

genetree.folder = "file/path/to/folder/of/genetrees"
taxa.delete = c("species_one", "species_two")
save.name = "test-dataset"

setupAstral(genetree.folder = genetree.folder,
            output.name = save.name,
            overwrite = TRUE,
            taxa.remove = taxa.delete,
            min.n.samples = 4,
            min.sample.prop = 0.1,
            make.polytomy = TRUE,
            polytomy.limit = 10)

runAstral(input.genetrees = save.name,
          output.name = save.name,
          astral.path = astral.path,
          astral.t = 2,
          quiet = F,
          load.tree = FALSE,
          multi.thread = TRUE,
          memory = "8g")

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