[Bioperl-l] SimpleAlign and consensus_string

[Amin Momin]

Hi ,

I am generating a consensus sequence by aligning two protein homologs
using Bio::Tools::Run::Alignment::TCoffee. However, I am unable to
understand the criteria consensus_string() method of simpleAlign uses
to determine the consensus at position with dissimilar aminoacids/
nucleotide. Also how would the % cutoffs provided to
consensus_string() affect the outcome.


Thanks,
Amin