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» BLAST 
NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
http://www.ncbi.nlm.nih.gov/BLAST/
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» ESPript
Formating of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry.
http://prodes.toulouse.inra.fr/ESPript/ESPript/index.php
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» GWBLAST
Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities.
http://www.imtech.res.in/raghava/gwblast/
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» 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.
http://www.ch.embnet.org/software/GMFDF_form.html
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» 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
http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
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» Interactive Blast Query
Utility for online manipulation of Blast results. Results organized in a table format.
http://www.aridolan.com/biq/Query.aspx
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» Meta-MEME
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
http://metameme.sdsc.edu/
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» PatternHunter
Commercial general homology search software significantly faster than BLAST.
http://www.bioinformaticssolutions.com/products/ph/
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» 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.
http://www.cse.ucsc.edu/research/compbio/sam.html
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» 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.
http://www.isrec.isb-sib.ch/
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» WU-BLAST Archives
Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis.
http://blast.wustl.edu
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