asap_tbl: A Command-Line Interface for ASAP - Assemble Species by...
In delimtools: Helper Functions for Species Delimitation Analysis

asap_tbl

R Documentation

A Command-Line Interface for ASAP - Assemble Species by Automatic Partitioning

Description

asap_tbl() returns species partition hypothesis estimated by ASAP software https://bioinfo.mnhn.fr/abi/public/asap/.

Usage

asap_tbl(
  infile,
  exe = NULL,
  haps = NULL,
  model = 3,
  outfolder = NULL,
  webserver = NULL,
  delimname = "asap"
)

Arguments

`infile`	Path to fasta file.
`exe`	Path to an ASAP executable.
`haps`	Optional. A vector of haplotypes to keep into the tbl_df.
`model`	An integer specifying evolutionary model to be used. Available options are: 0: Kimura-2P 1: Jukes-Cantor (default) 2: Tamura-Nei 3: simple distance (p-distance)
`outfolder`	Path to output folder. Default to NULL. If not specified, a temporary location is used.
`webserver`	A .csv file containing ASAP results obtained from a webserver. Default to NULL.
`delimname`	Character. String to rename the delimitation method in the table. Default to 'asap'.

Details

asap_tbl() relies on system to invoke ASAP software through a command-line interface. Hence, you must have the software available as an executable file on your system in order to use this function properly. asap_tbl() saves all output files in outfolder and imports the first partition file generated to Environment. Alternatively, asap_tbl() can parse a .csv file obtained from webserver such as https://bioinfo.mnhn.fr/abi/public/asap/asapweb.html.

Value

an object of class tbl_df

Author(s)

Nicolas Puillandre, Sophie Brouillet, Guillaume Achaz.

Source

Puillandre N., Brouillet S., Achaz G. 2021. ASAP: assemble species by automatic partitioning. Molecular Ecology Resources 21:609–620.

Examples




#' # get path to fasta file
path_to_file <- system.file("extdata/geophagus.fasta", package = "delimtools")

# run ASAP
asap_df <- asap_tbl(infile = path_to_file, exe= "/usr/local/bin/asap", model= 3)

# check
asap_df

delimtools documentation built on April 3, 2025, 9:28 p.m.