CIPRES may be about to have a data handling overhaul. If you haven’t clicked around on the CIPRES site do so, its great.
Cyberinfrastructure for Phylogenetic Research (CIPRES) project is an open collaboration funded by the National Science Foundation…The goal of the CIPRES project is to enable large-scale phylogenetic reconstructions on a scale that will enable analyses of huge data sets containing hundreds of thousands of bio molecular sequences.
I mostly use the RAxML implementation at the CIPRES Portal. This runs jobs on the San Diego Supercomputer Centre rather than my desktop.
I have recently found SWAMI which is an online workbench for different types of sequence analysis. There are several sites like this already out there but SWAMI is new and seems nicely designed. They allow you to make suggestions about new services to add and got back to me quickly when I requested several packages be added (RAxML, MUSCLE, transAlign). They also said something interesting in the email to me-
“The ther tools you mentioned are in progress, or will be added to the list. However, I will include those in the NGBW, but we plan to launch those in a separate site for phyolgenetics called the CIPRES Portal in a month or so. The CIPRES portal exists, but it will be inheriting the login, data storage area etc, and will be able to provide a much higher end computing capacity for serious systematists with large data sets.”
Sounds good. I assumed the “much higher capacity” is compared to SWAMI rather than CIPRES, but being able to store data, pre-process and manipulate at CIPRES will be useful. SWAMI still has some rough edges but it looks like improvements are happening fast. All my niggles were mentioned in FAQs or tutorials as about to be fixed (in the August 2008 update).