mptp_tbl: A Command-Line Interface for mPTP - multi-rate Poisson Tree...

In delimtools: Helper Functions for Species Delimitation Analysis

A Command-Line Interface for mPTP - multi-rate Poisson Tree Processes

Description

mptp_tbl() returns species partition hypothesis estimated by mPTP software https://github.com/Pas-Kapli/mptp.

Usage

mptp_tbl(
  infile,
  exe = NULL,
  outfolder = NULL,
  method = c("multi", "single"),
  minbrlen = 1e-04,
  webserver = NULL,
  delimname = "mptp"
)

Arguments

infile	Path to tree file in Newick format. Should be dichotomous and rooted.
exe	Path to an mPTP executable.
outfolder	Path to output folder. Default to NULL. If not specified, a temporary location is used.
method	Which algorithm for Maximum Likelihood point-estimate to be used. Available options are: single Single-rate PTP model. It assumes that every species evolved with the same rate. multi Multi-rate mPTP model. It assumes that all species have different evolutionary rates.
minbrlen	Numeric. Branch lengths smaller or equal to the value provided are ignored from computations. Default to 0.0001. Use min_brlenfor fine tuning.
webserver	A .txt file containing mPTP results obtained from a webserver. Default to NULL.
delimname	Character. String to rename the delimitation method in the table. Default to 'mptp'.

Details

mptp_tbl() relies on system to invoke mPTP 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. mptp_tbl() saves all output files in outfolder and imports the results generated to Environment. If an outfolder is not provided by the user, then a temporary location is used. Alternatively, mptp_tbl() can parse a file obtained from webserver such as https://mptp.h-its.org/.

Value

an object of class tbl_df

Author(s)

Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlides, Alexandros Stamatakis, Tomáš Flouri.

Source

Kapli T., Lutteropp S., Zhang J., Kobert K., Pavlidis P., Stamatakis A., Flouri T. 2016. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630-1638.

Examples

# get path to phylogram
path_to_file <- system.file("extdata/geophagus_raxml.nwk", package = "delimtools")

# run mPTP in single threshold mode (PTP)
ptp_df <- mptp_tbl(
  infile = path_to_file,
  exe = "/usr/local/bin/mptp",
  method = "single",
  minbrlen = 0.0001,
  delimname = "ptp",
  outfolder = NULL
)

# check
ptp_df

# run mPTP in multi threshold mode (mPTP)

mptp_df <- mptp_tbl(
  infile = path_to_file,
  exe = "/usr/local/bin/mptp",
  method = "single",
  minbrlen = 0.0001,
  delimname = "mptp",
  outfolder = NULL
)

# check
mptp_df

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