setupAstral: setupAstral

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

setupAstral

Description

This function sets up an astral run from gene trees

Usage

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

Arguments

genetree.folder	a folder of genetrees to prepare for astral analyses
output.name	the save name for your concatenated gene tree file
overwrite	whether to overwrite an existing dataset
taxa.remove	species that you would like removed from each gene tree
min.n.samples	the minimum number of samples to keep a gene tree
min.sample.prop	the minimum proportion of samples to keep a gene tree
make.polytomy	whether to collapse poorly supported nodes into polytomies
polytomy.limit	if make.polytomy = TRUE, the threshold value for node collapsing

Value

the function goes through each gene tree and applies the desired filters. It then writes all the gene trees that pass the filters to a single file for use in ASTRAL-III.

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)

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