multiple sequence alignment

Jason Miller millerj at
Sat Nov 11 21:09:08 EST 1995

Thanks everybody. I asked for help finding a survey of multiple sequence
alignment software. Many people responded by e-mail. Many others asked me
to post results. Here are the responses (anonymous since they were

-- Jason Miller, University of Pennsylvania, millerj at

here is a couple of references that could be of interest for you:

Record 1 of 3 - MEDLINE (R) 1994

TI: Comparative analysis of multiple protein-sequence alignment methods.
AU: McClure-MA; Vasi-TK; Fitch-WM
SO: Mol-Biol-Evol. 1994 Jul; 11(4): 571-92

Record 2 of 3 - MEDLINE (R) 1/95-11/95

TI: Comprehensive study on iterative algorithms of multiple sequence alignment.
AU: Hirosawa-M; Totoki-Y; Hoshida-M; Ishikawa-M
SO: Comput-Appl-Biosci. 1995 Feb; 11(1): 13

You might look up papers by Martin Vingron who looked at various methos
and the effects of different gap penalties. Meth Enz. Vol 183 has a lot of
relevant stuff. Gaston Gonnet put out a paper in Science a few years back
claiming to have the ultimate solution. IMHO different methods work for
different classes of problem, much as one might not like it. 

Clustal V in unix and DOS environment. It performes multiple alignment.
Protein Sequence Alignment and Database Scanning (Geoffrey Barton)

You will find informations and links to multiple alignment programs on the
BioComputing Hypertext Coursebook at:

Consider wavelet models.  It may work.  MATHLAB(R) may do the job.
Discussion Theme: The MSA algorithm

A Gentle Guide to Multiple Alignment, (Georg Fuellen)

Multiple Sequence Alignments (Fredj Tekaia)

ClustalW tutorial, (Fredj Tekaia)

ClustalW tutorial, (Andrew T. Lloyd)

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