Description Usage Arguments Details Examples
Run the Accurate Species TRee ALgorithm for inferring species trees from gene trees under the multi-species coalescent model.
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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. |
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
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | # 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')
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