| 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. |
Classical
