Problem with pretty -dif -cons

Grundschober grund at cmu.unige.ch
Wed Jun 28 09:24:11 EST 1995

Hello folks,
I trying to use pretty on a pileup of 30 sequences. As I want the
consensus and only the differences from it to be shown I use the commands:
-dif -cons.
The output looked nice, unfortunately when I checked the result there were
some errors:
some differences from the consensus didn't show up although they were
present in the pileup file (I checked !).

 This happened with nucleotide sequences and amino acid sequences as well.
I tried to play with the threshold and plurality settings with no effect
on the errors.

Does somebody have an explanation and a solution?

Thank you very much.

C. Grundschober
Transplantation Immunology Unit
Centre Medical Universitaire
1211 Geneve 4

grund at cmu.unige.ch

More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net