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:
The output looked nice, unfortunately when I checked the result there were
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.
Transplantation Immunology Unit
Centre Medical Universitaire
1211 Geneve 4
grund at cmu.unige.ch