Sorry if this is a stupid question, I'm new this type of analysis. I input my sequence alignment of 516 codons long, and after analysis, I get a list of sites that is only 502 long. There are number of regions where there is multiple gaps in the alignment. Could you tell me how I can correlate selected codons back to my sequence? Thanks in advance.

Dear Evan,


wrote on Jan 13^th, 2006 at 1:42pm:

Sorry if this is a stupid question, I'm new this type of analysis. I input my sequence alignment of 516 codons long, and after analysis, I get a list of sites that is only 502 long. There are number of regions where there is multiple gaps in the alignment. Could you tell me how I can correlate selected codons back to my sequence? Thanks in advance.

This is odd; datamonkey does not filter gaps from the alignment. If you upload 516 codons and the file is accepted, the analyses should return 516 codons as well. Could you e-mail your input file to help at datamonkey dot org so that I can reproduce the conditions you report?

Cheers,
Sergei