Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.

ABSTRACT: Over the years, there have been claims that evolution proceeds according to systematically different processes over different timescales and that protein evolution behaves in a non-Markovian manner. On the other hand, Markov models are fundamental to many applications in evolutionary studies. Apparent non-Markovian or time-dependent behavior has been attributed to influence of the genetic code at short timescales and dominance of physicochemical properties of the amino acids at long timescales. However, any long time period is simply the accumulation of many short time periods, and it remains unclear why evolution should appear to act systematically differently across the range of timescales studied. We show that the observed time-dependent behavior can be explained qualitatively by modeli

SUBMITTER: Kosiol C 

PROVIDER: S-EPMC3157587 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature