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

Usage

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

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.

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'.

Value

an object of class tbl_df

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.

Author

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

Examples

# \donttest{

#' # 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
)
#> Error in abgd_tbl(infile = path_to_file, exe = "/usr/local/bin/abgd",     model = 3, slope = 0.5, outfolder = NULL): Error: Please provide a valid path to the ABGD executable file.

# check
abgd_df
#> Error: object 'abgd_df' not found
# }