PLEX - Phylogenetics, Likelihood, Evolution, and Complexity version 0.95 - beta version Authors: A.P. Jason de Koning, Wanjun Gu and David Pollock jason.de.koning@gmail.com http://jasondk.org David.Pollock@UCDenver.edu http://www.evolutionarygenomics.com This program was created and distributed by the David Pollock laboratory, University of Colorado School of Medicine copyleft Ⓚ 2012 David Pollock All rites reversed. http://www.evolutionarygenomics.com Dept. Biochemistry & Molecular Genetics 12801 17th Ave., MS 8101 PO Box 6511 Aurora, CO 80045 This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Changes since version 0.81a: - several bug fixes related to initialization - nucleotide model now runs a GTR with proposals empirically tuned for the Mam_CYTB_v4.reduced.noGaps.noAmbig.fasta dataset, as in de Koning et al (2009) - made a fix to the incomplete data logL calculation - experimental OpenMP code disabled to allow compilation on systems without OMP - removed sse4 features from Makefile to increase compatibility with older systems Changes since version 0.81b: - fixed output of branchlengths so they are summed correctly over segments - added branch labels to treeoutfile - added output of substitution counts by several methods (see controlfile in ./examples, referring to 5taxon.fasta example dataset) Changes since version 0.81c: - additional site-specific substitution count output: mode 3 = based on branch end-points; 4 = based on pathway sampled along transient points Changes since version 0.81d: - added error checking for when sequence names and tree names may mismatch - fixed bugs in removal of gapped columns - fixed some initialization issues for ancestral states Changes since version 0.81e: - fixed output of terminal branch node ids in treeoutfile and subsoutfile - fixed a rare bug when new branch segments weren't initialized properly (led to 'beta out of bounds' errors) - compiling with full optimizations should no longer lead to intermittent errors - rate variation fixes Changes since version 0.81g: - slice sampling - flexible priors - coevolution simulation options (many) - others This is an unfinished experimental beta pre-release. Not everything works and the program may be temperamental. FASTA format is expected for input. Please email Jason to register your interest if you'd like to be notified of updates. QUICK START GUIDE: To compile: cd src make Options to control the model used, data files, and MCMC options are in 'controlfile'. To run, you will need a controlfile, sequence alignment (FASTA format), and a treefile (Newick format). Examples are provided in ./examples: cd ../working cp ../examples/* ./ cp ../scripts/* ./ cd ../working ./PLEX Some hints: The default datafile and control file runs a general non-reversible amino-acid substitution model. To use the scripts, copy them into your current folder as in the above example. * NOTE: For each of these script examples below, the # 1 refers to the number of burnin generations * To examine incomplete-data log likelihoods over time: perl plotInLikelihood.pl 1 likelihoodfile To examine complete-data log likelihoods over time: perl plotLikelihood.pl 1 likelihoodfile To examine a posterior rate matrix summary: perl posteriorSummary.pl 1 matrixoutfile NOTE: these scripts assume you have R installed and are using a Mac. Minor errors may be generated on Linux, as the scripts attempt to open windows with plots in a Mac-specific way. For details of the core underlying methods see: de Koning, Gu, and Pollock (2010). Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. MBE (and references therein) For any questions please contact Jason (Jason.de.Koning@gmail.com)