MSF as input to plotsimilarity

Mike Neubauer neubauer at bms.com
Thu Dec 1 19:38:01 EST 1994

In article 11466 at emba.uvm.edu, brianf at med.uvm.edu (Brian Foley) writes:
>	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?
   You must designate which sequences in the file pileup.msf are to be used by PLOTSIMILARITY.  You can select all of the sequences in the msf file by giving


the {*} (left-curly-q asterisk right-curly-q) designates all of the sequences in your file pileup.msf

good luck

Mike Neubauer

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