RepMaker RepMaker is a simple perl utility for automatically generating multiple NEXUS files. Files can be used to distribute a single PAUP* bootstrap analysis over multiple machines using a scheduler, such as, Condor or the perl utility BsLauncher (included with RepMaker). RepMaker is available free of charge on the web.

MMML (Mixed Model Maximum Likelihood)

MMML is a simple perl program designed to facilitate mixed model maximum likelihood analysis (hence the name MMML). The primary analysis engine is PAUP*; therefore, PAUP* must be installed on your system and the binary must be in you path. The program uses the Parallel ForkManager perl model to take advantage of systems with multiple CPUs. The Parallel ForkManager is available for freehere . Contact me me for a copy of this script.

AWTY (Are We There Yet) 

AWTY is a system for graphical exploration of Markov chain Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. The graphics produced by AWTY are designed to help assess whether an MCMC analysis has run long enough, such that tree topologies are being sampled in proportion to their true posterior probability distribution. In other words, "Are We There Yet?" or AWTY for short.
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This project was originially entended to compare corrected versus uncorrected boostrap methods but then was expanded to compare various heuristic short cuts and how they might effect the bootstrap support values. As long as we were going there we figured we'd look at split posteriors from MCMC analyses.