Dear colleagues,
I am working on a plant protein, Class III chitinase. By selection test (dN/dS), it looks under strong purifying selection pressure. Can I say such protein might be functional important based on the selection test result?
Can any one suggest a program other than PAML and Mega which could be used for coding sequence selection test? I am a layman in this field, I hope the program could be easy-to-use.
Best
Zha
Zha,
I would advise you to read "The altered evolutionary trajectories of gene duplicates"
http://www.cell.com/trends/genetics/abstract/S0168-9525(04)00250-1?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0168952504002501%3Fshowall%3Dtrue&cc=y=
"Selection in the evolution of gene duplications" http://download.springer.com/static/pdf/181/art%253A10.1186%252Fgb-2002-3-2-research0008.pdf?originUrl=http%3A%2F%2Fgenomebiology.biomedcentral.com%2Farticle%2F10.1186%2Fgb-2002-3-2-research0008&token2=exp=1464987024~acl=%2Fstatic%2Fpdf%2F181%2Fart%25253A10.1186%25252Fgb-2002-3-2-research0008.pdf*~hmac=b336e5cc0123e039cd1f2d5cb9b4510c9a024fbeb5e5817b8a8cc301bba6607c
and "Maximum likelihood methods for detecting adaptive evolution after gene duplication"
http://link.springer.com/chapter/10.1007/978-94-010-0263-9_20
for programs: look at JCoDA (Java Codon Delimited Alignment) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887424/
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