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
Switzerland
grund at cmu.unige.ch
