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In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is(More)
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume that all samples are tips, they do not allow for this possibility. We have developed and implemented a Bayesian Markov(More)
— The total evidence approach to divergence-time dating uses molecular and morphological data of extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the(More)
This peer-reviewed article can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in Algorithms for Molecular Biology are listed in PubMed and archived at PubMed Central. permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background
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