How To Select Homologous Regions Based On An Alignment

Question

[sanchezcavani]

I have generated a multiple sequence alignment. Now I want to extract the really homologous region within the alignment. I think the best way is to manually check it. However it does not seem possible if a large number of sequences are being analyzed. Does anyone know what tools I could use to generate the regions with high quality of alignment?

Answer 1

[David Westergaard]

Why not just compute a score for each position in the alignment (e.g. entropy), and then extract those regions with high scores?

[Ashutosh Pandey]

Just for an idea about Shannons entropy: http://bio.dfci.harvard.edu/Tools/svs_help.html