I am trying to analyse APC gene. I used blast to get multiple sequence alignment. How many sequences should I choose to input in Align GVGD. Is there any criteria?
The number of sequences is less important than the diversity range of the sequences chosen, and perhaps somewhat dependent on the selection pressures and population sizes of the organisms involved. The GVGD software is aiming to calculate site-specific selection pressures on each codon or amino acid in a protein. Other programs such as the adaptive evolution server at http://www.datamonkey.org/ are also very useful for this type of analysis.