Many of us have seen desktop computers with a note pasted on them saying "Do not use computer: doing phylogenetic analysis. Thanks, Charlie". There are now many ways to scale up analyses, many of which run for free on someone else's supercomputer. It sounds too good to be true, but that's tax dollars at work (and not just US taxes). There will be a NIMBios tutorial about this in Fall 2010. Here are some preliminary links to resources:
- CIPRES portal: This is a free interface to a supercomputer that lets you do MrBayes, PAUP, RAxML, POY, Garli, and other analyses.
- Mobyle: Automated analysis lets you go all the way from alignment to tree search to tree visualization.
- Phylogeny.fr: Similar capabilities as Mobyle
- Phylota browser: has aligned sequences from GenBank and done preliminary trees for many groups.
- PhyLIS: a distribution of linux already loaded with useful phylogenetic software. An easy way to interact with the versions of software that might be running on other clusters. You can burn it onto a CD and run it off that (no need to modify your computer), or you could put it in Sun VirtualBox and run it contained by itself while the rest of your computer stays in your normal Mac/Windows OS.