A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process c...
AbstractGaphyl is an application of evolutionary algorithms (EA's) to phylogenetics, an approach used by biologists to investigate evolutionary relationships among organisms. ...
We investigate maximum likelihood parameter learning in Conditional Random Fields (CRF) and present an empirical study of pseudo-likelihood (PL) based approximations of the paramet...
Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the maximum likelihood method is computationally extremely expensive. In previous work,...
Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets fro...