BLAST: NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
ESPript: Formating of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry.
GeneMatcher: Access to Smith-Waterman-based FDF sequence comparison program, with excellent explanation of when to use it vs. BLAST - from the Univ. of Lausanne, FR.
GeneStream II: Sequence comparision and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch) - from the IGH, Montpellier FR.
GWBLAST: Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities.
HMM library for all proteins of known structure: This is a server for structural superfamily assignments to protein sequences using Hidden Markov Models. The services included are: -homology searching -alignments -genome assignments
Interactive Blast Query: Utility for online manipulation of Blast results. Results organized in a table format.
Meta-MEME: Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
mreps : maximal tandem repeats search: Open source tool for identifying serial repeats (tandem repeats) in DNA sequences.
PatternHunter: Commercial general homology search software significantly faster than BLAST.
Sequence Alignment and Modeling System: Implementation of hidden Markov models for sequence analysis. Free UNIX software for nonprofit groups, and sequences can be submitted online.
The ISREC Group Servers: Detection and assessment of similarity between distantly related sequences by means of a variety of remotely-executable software - from the Swiss Inst. for Experimental Cancer Research.
WU-BLAST Archives: Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis.