astral: astral

In DomBennett/om..astral: Outsider module for running astral

Description

Run the Accurate Species TRee ALgorithm for inferring species trees from gene trees under the multi-species coalescent model.

Usage

astral(
  input_file,
  output_file = "astral_species.tre",
  log_file = NULL,
  java_args = NULL
)

Arguments

input_file	File path to list of Newick trees.
output_file	File path to where resulting species tree should be saved.
log_file	File path to where log should be saved. If NULL, no log is saved.
java_args	Extra arguments for Java, character vector.

Details

Online documentation for the original program can be found here https://github.com/smirarab/ASTRAL.

input_file and output_file are equivalent to the arguments '-i' and '-o', respectively.

See online for details on input_file formatting.

Change memory settings with -Xmx#M in java_args.

Examples

# import
library(outsider)
astral <- module_import('astral', repo = 'dombennett/om..astral')

# data
# test dataset of song mammals
url <- 'https://raw.githubusercontent.com/DomBennett/om..astral/master/test_data/song_mammals.424.gene.tre'
input_file <- file.path(tempdir(), 'song_mammals.424.gene.tre')
download.file(url = url, destfile = input_file)

# run with test file and 1GB memmory
output_file <- file.path(tempdir(), 'song_mammals.tre')
log_file <- file.path(tempdir(), 'log_song_mammals.txt')
astral(input_file = input_file, output_file = output_file, log_file = log_file,
       java_args = '-Xmx1000M')

DomBennett/om..astral documentation built on Jan. 19, 2020, 10:29 a.m.