[Bioperl-l] how to get consensus_iupac from dna alignment that has lot of iupac ambiguity codes?

Bhakti Dwivedi bhakti.dwivedi at gmail.com
Wed Feb 10 23:57:34 EST 2010


Hi,

I am trying to make a consensus for the nucleotide sequence alignment.
 The alignment sequences, however contain a lot of
IUPAC ambiquity codes.  And this seems to throw off an error message
(indicating that it is a protein sequence) when I use
consensus_iupac().
How can I fix this?  Do I have to manually define the dna iupac alphabets?

I will appreciate any kind of help. Thanks!

Bhakti


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