A brief digest follows of paraphrased responses to my request for PC/Mac
programs for comparing sequences and constructing phylogenetic trees.
Thanks to those who kindly supplied this information.
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The most widely used sequence alignment program is CCLUSTAL. Runs on PCs.
A selfextractable file can be obtained by anonymous FTP from
ftp.ebi.ac.uk.
unix pub/software/unix/clustalw.tar.Z (compressed tar archive)
vms pub/software/vms/clustalw.uue (uuencoded ZIP archive)
mac pub/software/mac/clustalw.sea.hqx (self extracting
archive/binhex)
PC pub/software/dos/clustal$.exe (self extracting ZIP archive)
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The FASTA package, in particular SSEARCH and ALIGN, will do alignments.
Available for Unix, DOS, and Mac's from: ftp.virginia.edu in pub/fasta.
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Felsenstein's PHYLIP package is available for Mac. Also one for
Swofford's PAUP. Check a bionet ftp sites. [n.b.: Felsenstein has WWW
page: do net search on "Phylip." Includes info on other phylogenetic
programs.]
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VOSTORG package at anonymous FTP at
gsbs18.gs.uth.tmc.edu/pub/zharkikh/vostorg
For IBM; has simple level of phylogenetic analysis. Includes sequence dot
matrix
comparison. alignment, distance matrix calculation and tree
reconstruction/ visualisation. It was used at our graduate courses and in
routine practice.
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DAPSA. Contact HARLEY at chempath.uct.ac.za for more info.
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SeqPup, which when combined with ClustalW for
automatic alignment, is a free tool for biosequence analyses.
Fetch it at
<ftp://iubio.bio.indiana.edu/molbio/seqpup/>
<gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
<http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>
Caveat: it is still undergoing development, and its incomplete
state may make it unsuited for your need just now. It will be
better off in a few months.
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There is DCSE (Dedicated Comparative Sequence Editor) for DOS. It does
what
you want, though the Unix versions are a lot nicer. You might consider
using Linux to run Unix programs on your PC. You can find more info on and
the distributions of DCSE on URL:
http://www-rrna.uia.ac.be/~peter/dcse
or use anonymous ftp to host indigo2.uia.ac.be
