Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the ...
The paper: M.C. Brandley et al., "Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards," Systematic Biol, 54:373-90, 2005. (Cited in 73 papers) The ...
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