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DNA/Protein Sequence Analysis

Dave Carmean carmean at sfu.ca
Fri Mar 24 22:10:41 EST 1995

I keep my sequence data in SeqApp.  This allows me to import and export
many file formats from a standard file of aligned sequences. I can produce
PAUP and PHYLIP files quickly, as well as do BLAST searches.  I print
alignments by exporting the file as a PAUP file.  In SeqApp, I can
translate sequences to amino acids and use Dotty plot to compare the
similarity between two sequences.

You will hear many complaints about SeqApp because it is buggy and will
crash.  However, by knowing to avoid certain keystrokes (e.g. command-F),
and not expecting more than I know it will do, I have not had any problems
with it.  SeqApp will only show the first 2700 basepairs in the alignment
window, but all of the sequence is visible in the single sequence window.

I enter data from autorads using Seqspeak.  I use CLUSTAL-V to initially
align sequences and SeqApp for final alignment.  

SeqApp (by Don Gilbert), Seqspeak, and Clustal are available from 
FTP.BIO.indiana.edu  by gopher or anonymous FTP.  PHYLIP is available by
anonymous FTP (from Joe Felsenstein) at

I do parsimony analyses in PAUP (by Dave Swofford, to be distributed by
Sinauer?), and use PHYLIP for maximum likelihood, neighbor joining, etc. 
MacClade (by Dave & Wayne Maddison, from Sinauer) is excellent for
analysis of the evolution of characters.

I have made a help sheet for SeqApp.
Cheers to your data,
Dave Carmean                     carmean at sfu.ca
Biological Sciences              (604) 291-5625   FAX  291-3496
Simon Fraser University          
Burnaby, BC  CANADA V5A 1S6

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