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Separating out the consensus from lineup

Jack Kramer kramer at oj.rsmas.miami.edu
Thu Feb 17 08:31:32 EST 1994


In article <2jrgdf$pb0 at gaia.ucs.orst.edu>,
Malin Masreliez <masrelia at ava.bcc.orst.edu> wrote:
>
>I was wondering if there is an easy way to save the consensus
>sequence generated by lineup in a separate file (in GCG format)
>so it can be used as input to other programs.  Editing the
>alignment file is a drag...
>

The "/UGLY" command line switch for the PRETTY command will do
what you want.  You may still need to use SEQED to delete the
gaps to use the seqeunce in some other programs.

Jack Kramer




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