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.
WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
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. “
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454.
TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.