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mothur
Mothur addresses the bioinformatics needs of the microbial ecology community. Functionality such as dotur, sons, treeclimber, s-libshuff, unifrac, and other algorithms are provided. In addition to improving the flexibility of these algorithms, a number of other features including calculators and visualization tools offers the ability to go from raw sequences to the generation of visualization tools.
diyabc
Approximate Bayesian Computation for inference on population history using molecular markers.