HMMER User's Guide

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Other profile HMM implementations

Several implementations of profile HMM methods and related PSSM methods are available. Some are listed in the table below.

Software	URL
HMMER	http://hmmer.wustl.edu/
SAM	http://www.cse.ucsc.edu/research/compbio/sam.html
PFTOOLS	http://ulrec3.unil.ch:80/profile/
HMMpro	http://www.netid.com/html/hmmpro.html
GENEWISE	http://www.sanger.ac.uk/Software/Wise2/
PROBE	ftp://ncbi.nlm.nih.gov/pub/neuwald/probe1.0/
META-MEME	http://www.cse.ucsd.edu/users/bgrundy/metameme.1.0.html
BLOCKS	http://www.blocks.fhcrc.org/
PSI-BLAST	http://www.ncbi.nlm.nih.gov/BLAST/newblast.html

HMMER, SAM, PFTOOLS, and HMMpro are the most closely related to the profile HMM methods introduced by Krogh et al. HMMpro is commercial, not free software.