Phylogenetic analysis is a very computing-intensive process and very often requires supercomputing facilities. The CIPRES (Cyberinfrastructure for Phylogenetic Research) supercomputing facility based in San Diego is one of the most powerful facilities to run phylogenetic analyses for large data sets, and it is FREE! A variety of programs are available. They generally work quite well. However, one the programs frequently used for molecular dating, called 'BEAST', runs rater slow at this site. A data set of 130 taxa running for 10-million generations would take 7 hours to finish. This is even longer than running on a powerful desktop computer such as a PowerMac or a PC tower. What's more, a BEAST analysis are usually run for a 100 million generations, which would require 70 hours or four days for the CIPRES site to complete. Multiple runs are generally needed to adjust input parameters and at this speed a thorough exploration of one's data set would require up to a month of a few months.
Alternatives would be setting up access to a local cluster service. Many universities have such facilities, but often charge a fee to use.
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