Models of Sequence Evolution for DNA Sequences Containing Gaps

摘要: Most evolutionary tree estimation methods for DNA sequences ignore or inefficiently use the phylogenetic information contained within shared patterns of gaps. This is largely due to computational difficulties in implementing models insertions and deletions. A simple way incorporate this treat a gap as fifth character (with four nucleotides being other four) it Markov model nucleotide substitution. idea has been dismissed past, since treats multiple-site insertion deletion sequence independent events rather than single event. While true, we have found that under many circumstances better inadequately it, at least topology estimation. We propose an extension class substitution show that, data sets (both real simulated) with short medium gaps, these do lead effective also implement ad hoc method which likelihood columns containing gaps downweighted order avoid giving them undue influence. The precision estimated tree, assessed using chain Monte Carlo techniques find posterior distribution over space, improves five-state compared standard effectively