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polyphred
PolyPhred is a program that compares fluorescence-based sequences.
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.