Comparison of protein phylogeny reconstruction methods using natural protein sequences
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- Krivozubov, M.S. & Spirin, S.A. Moscow Univ. Biol.Sci. Bull. (2010) 65: 139. doi:10.3103/S0096392510040036
Comparison of several protein phylogeny reconstruction methods was realized on a set of natural protein sequences. The programs of the PHYLIP package and FastME, PhyML and TreeTop programs were tested. In contrast to several studied programs that used simulated sequences, our results demonstrate the superiority of distance methods over the maximum likelihood method.