abgd_tbl: A Command-Line Interface for ABGD - Automatic Barcode Gap...

In delimtools: Helper Functions for Species Delimitation Analysis

A Command-Line Interface for ABGD - Automatic Barcode Gap Discovery

Description

abgd_tbl() returns species partition hypothesis estimated by ABGD software https://bioinfo.mnhn.fr/abi/public/abgd/.

Usage

abgd_tbl(
  infile,
  exe = NULL,
  haps = NULL,
  slope = 1.5,
  model = 3,
  outfolder = NULL,
  webserver = NULL,
  delimname = "abgd"
)

Arguments

infile	Path to fasta file.
exe	Path to an ABGD executable.
haps	Optional. A vector of haplotypes to keep into the tbl_df.
slope	Numeric. Relative gap width (slope). Default to 1.5.
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 .txt file containing ABGD results obtained from a webserver. Default to NULL.
delimname	Character. String to rename the delimitation method in the table. Default to 'abgd'.

Details

abgd_tbl() relies on system to invoke ABGD 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. abgd_tbl() saves all output files in outfolder and imports the first recursive partition file generated to Environment. Alternatively, abgd_tbl() can parse a .txt file obtained from a webserver such as https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html.

Value

an object of class tbl_df

Author(s)

N. Puillandre, A. Lambert, S. Brouillet, G. Achaz

Source

Puillandre N., Lambert A., Brouillet S., Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21(8):1864-77.

Examples

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

# run ABGD
abgd_df <- abgd_tbl(
  infile = path_to_file,
  exe = "/usr/local/bin/abgd",
  model = 3,
  slope = 0.5,
  outfolder = NULL
)

# check
abgd_df

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