Supercomputers or computing clusters are now a popular solution to the computational challenges posed by increasingly large phylogenetic datasets. By using a cluster, you can speed a typical MrBayes run up by at least eight times (by running each of the eight chains required by the default MCMCMC settings on a different processor). The obvious problem with these resources, of course, is that many users don't have access to a cluster. Fortunately, this is beginning to change. One emerging resource is the CIPRES portal, which offers public access to computing resources at the San Diego Supercomputing Center. Although some have complained that this massively multi-PI, NSF-funded resource has been slow to develop, there has been tangible and important progress over the past few years. At this point, users can implement some of the most popular applications in phylogenetics (e.g., PAUP*, MrBayes, RaxML) through a web interface. In most cases, unfortunately, this interface is limiting; for example, some of the most popular options in MrBayes (e.g., parititioning) and PAUP* (e.g., multiple randomized sequence addition replicates in a heuristic search) are remain unavailable. Nevertheless, they're aware of these limitations and I've been told that improvements are on the horizon. This is an important resource and I want very much for it to succeed.
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