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MultiPipMaker
MultiPipMaker
is a multiple sequence alignment tool. Thhis program can be used with
this web
interface.
ClustalW / ClustalX
ClustalW
is a multiple sequence alignment program from EBI. The windows
version and unix
version stand-alone program can be downloaded from EBI.
ClustalX is the GUI version of ClustalW. The Windows
version and UNIX
version stand-alone program can be downloaded from EBI.
T-COFFEE
T-COFFEE is a multiple sequence alignment program. It is slower but
more accurate than other programs for sequences with less than 30% identity.
This program is used with this web
interface.
DIALIGN
DIALIGN is a DNA and protein sequence alignment program based on segment-to-segment
comparison. The following are two DIALIGN web interfaces:
http://bibiserv.techfak.uni-bielefeld.de/dialign/submission.html,
http://bioweb.pasteur.fr/seqanal/interfaces/dialign2-simple.html.
The program can also be used with this stand-alone
version.
Blocks Server
Blocks Server
is a service for biological sequence analysis at the Fred
Hutchinson Cancer Research Center in Seattle.
HMMER
HMMER is a freely
distributable implementation of profile hidden Markov models (profile
HMMs) software for protein sequence analysis.
MEME
MEME
is a tool for discovering motifs in a group of related DNA or protein
sequences.
MOTIF
MOTIF is a service
for searching protein and nucleic acid sequence motifs.
PatScan
PatScan
is a pattern matcher which searches protein or nucleotide (DNA, RNA,
tRNA etc.) sequence archives for instances of a pattern which you input.
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