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?
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sanchezcavani
Why not just compute a score for each position in the alignment (e.g. entropy), and then extract those regions with high scores?
Just for an idea about Shannons entropy: http://bio.dfci.harvard.edu/Tools/svs_help.html
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