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MSF file problem: solutions

B.L.Cohen gbga13 at udcf.gla.ac.uk
Tue Aug 2 08:00:36 EST 1994

Thanks to those who responded by e-mail and/or newsgroup to my question
about what could be wrong with my MSF files produced by Readseq either from
GDE or from SeqApp.   There were three problems, one file-specific and two
more general.

The file-specific problem affected taxon names, some of which were seen by
GCG Reformat as identical (they weren't, but they were over-long perhaps
and ended in the same character).

The general problems were:

1.  As Keith Robison has indicated, that alignment gaps were represented as
"-" and these got stripped out by Reformat, creating sequences of varying
length and hence unreadable (not to mention unaligned).   Replacing "_" by
"." by fair means or foul is an easy cure.

2.  The GDE MSF exported files had a Checksum, but it was not identical to
those calculated by Reformat, so without Reformatting these files would not
run in other programs such as Plotsimilarity even when the other problems
were cured.   The SeqApp MSF files had no checksum at all, or rather it was
= 0.

Thanks to Internet I also made contact with the computer support person in
the adjacent building (that says something!) and this speeded up finding
the solutions. 

I now have Plotsim output files on my desk.   To work!

What I need now (i.e. yesterday!) is a link between Plotsim and GDE so that
a mask can be automatically written into my alignment, based on any given
Plotsim output level, for the phylogenetic analyses that must ensue.   Did
I hear a volunteer?   Oh the joys of computing if you are completely
illiterate in the art!

Dr Bernard L. Cohen          Phone (+44) (0)41 339 8855 ext. 5103/5101
Genetics Dept.,              Fax               330 5994
University of Glasgow
Church St.,
Glasgow G11 5JS
Scotland, UK.

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