Given that an increasing share of statistical software in ecology and evolution is essentially free – e.g., open source and/or non-proprietary – I used to be bothered by the lack of suitable alternatives to PAUP* (which requires a licensing fee) for certain phylogenetic applications. Foremost among these is perhaps the ability to perform statistically rigorous phylogenetic model selection. There are now a number of free alternatives for phylogenetic model selection, that do not require PAUP* (which is required by the widely used Modeltest and MrModeltest programs ). I've probably been living in a bubble, because I just learned of several of these yesterday, but I thought I'd flag a few for Dechronization readers who might find this info useful.
One that I have used extensively is ModelGenerator , from the nice folks at the NUI Maynooth Bioinformatics Group. This is quite useful, not least because it has a web interface that lets you upload batches of fasta-formatted alignments. Because the computation is distributed across many “idle” desktop computers at NUI Maynooth, the processing time is low – I’ve uploaded batches of alignments only to get a results file emailed back to me within ~20 minutes or so. You can also run the program locally on your own machine or email the author for source. Additional options that I have yet to explore include jModeltest , FindModel (another web-based tool), and MrAIC . I'm sure this list is incomplete and welcome comments on programs I've missed as well as strengths and weaknesses of those I've listed.
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