parse_mPTP: Parse mPTP output for use with TaxCI

In eberlejonas/TaxCI: Calculate the Consistency Index and the Retention Index for taxonomic data

Description

Parse clustering output from mPTP (Kapli et al. 2016) for use with TaxCI.

Usage

parse_mPTP(file)

Arguments

file	Path to the mPTP output textfile containing the putative species clusters.

Value

A data.frame with two colums, the first containing specimen lables as in the taxonomic information and the second with integers describing cluster affiliation. Intended for use with BCCluster.

Author(s)

Jonas Eberle

References

P. Kapli, S. Lutteropp, J. Zhang, K. Kobert, P. Pavlidis, A. Stamatakis and T. Flouri (2016). Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo. bioRxiv preprint first posted online. doi: 10.1101/063875

See Also

BCCluster

Examples

# assuming that "mPTP_result.txt" is your mPTP output, use:
# df <- parse_mPTP("mPTP_result.txt")

eberlejonas/TaxCI documentation built on July 20, 2021, 9:46 a.m.