velvet

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Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454.

vsearch

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We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.

wise2

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Wise2 includes genewise, a program for aligning proteins or protein HMMs to DNA, and dynamite a rather cranky “macro language”” which automates the production of dynamic programming. “