Alignment Programs

High speed sequence comparison programs being considered for calculating similarity scores for the big all-by-all matrix.

diamond

• Article: http://www.nature.com/nmeth/journal/v12/n1/full/nmeth.3176.html
• website: http://ab.inf.uni-tuebingen.de/software/diamond/

afree

• Article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315314/

• website: http://static.vlsci.unimelb.edu.au/kmahmood/afree/

• code

  http://static.vlsci.unimelb.edu.au/kmahmood/EGM2/egm2_v1.zip

  http://static.vlsci.unimelb.edu.au/kmahmood/afree/afree_v2.0beta.zip

usearch

• Article: http://bioinformatics.oxfordjournals.org/content/26/19/2460.long
• website: http://drive5.com/usearch/