MSF as input to plotsimilarity

Brian Foley brianf at med.uvm.edu
Sun Nov 27 16:18:22 EST 1994

	The documentation says that the output created by PILEUP 
(the pileup.msf file) can be used as input to PLOTSIMILARITY.

	However, this is not working for me.  PLOTSIM says it cannot
read pileup.msf.  The documantation also says that all the sequences
have to be the same length, and my PILEUP was of sequences of
various lengths, gaps were introduced.  Could this be the problem?
If so, how does one plot the similarity of proteins that have
udergone deletions/insertions during evolution?

*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *

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