How to make Prettybox work?

Conrad Halling chhall at bb1t.monsanto.com
Fri May 13 15:07:55 EST 1994

In article <2qtmnh$osq at triton.unm.edu>, varela at unm.edu wrote:

> 	The PRETTYBOX program was just installed into our VAX computer
> containing the GCG software package, but it doesn't work.  Below is the
> apparent error message received when the program is run.   Questions: 1)
> what does the error message mean? 2) More importantly, what can be done to
> make it work?

[error message deleted]

> P.S.  _All_ file specifications do not work (i.e, @filename.fil, etc); the
> result is the same for each one.

Here is the first possibility:

PrettyBox is like Pretty in that it expects its input to be a GCG
sequence file in multiple sequence format (MSF).  PrettyBox does not
create the aligned sequences, it merely emphasizes the alignment.

You need to run PileUp first to create your alignment.  This will create
a file with a name something like PileUp.MSF.  Then run PrettyBox.
When it asks you for the sequences, enter PileUp.MSF{*}, just as you
would for Pretty.
Conrad Halling
Computational Molecular Biologist
Monsanto Co., St. Louis

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