Description

The PLEX package is designed to perform rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. The basic program is described in references listed below.

Downloading

PLEX is under continued development. The current version 0.95 zip file can be downloaded here. The distribution contains code, manual files, example data files with respective control files, and mac and unix compiled versions.

Manuals

This program is distributed under the Gnu Public LIcense in the hope that it will be useful, but WITHOUT ANY WARRANTY (see disclaimer).

Further information on using the program is available in a ReadMe file, a quick start guide, and an extended user manual.

Credits

Written and designed by APJ de Koning, W Gu and DD Pollock, with contributions to ancestral versions by Chip Jarred and Neeraja Krishnan.

References

A. P. J. de Koning, W. Gu, T. A. Castoe, and D. D. Pollock, “Phylogenetics, likelihood, Evolution and compleXity.” Bioinformatics, in review, (2012).

A. P. J. de Koning, Castoe, T. A., and D. D. Pollock, “Detection of Coevolution in Proteins with Phylogenetically-Integrated Mutual Information.” in prep (2012).

A. P. J. de Koning, Castoe, T. A., and D. D. Pollock, “RARdog: Rates Across Rates and Dependency Over Groups models.” in prep (2012).

A. P. J. de Koning, W. Gu, and D. D. Pollock, “Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories.” Molecular Biology and Evolution, Feb;27(2):249-65, (2010).

N. M. Krishnan, H. Seligmann, S. Z. Raina, and D. D. Pollock, “Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes.” DNA and Cell Biology, 23:707-714 (2004).

N. M. Krishnan, S. Z. Raina, and D. D. Pollock, “Analysis of among-site variation in substitution patterns.” Biological Procedures Online 6(1): 180-188  (2004).

Old Versions