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User application specific documentation is found on the following sites. Tufts cluster Application FAQ section details how to start the application.
blast
BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications.
mrbayes
MrBayes is a program for the Bayesian estimation of phylogeny.
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