Mathematical Framework for Phylogenetic Birth-And-Death Models

Details Mathematical Framework for Phylogenetic Birth-And-Death Models Mathematical Framework for Phylogenetic Birth-And-Death Models

2009-02-05

arxiv.org/abs/0902.0970v1

Biology

Quantitative Biology

Populations and Evolution

Scientific paper

A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in bioinformatics analyses for the inference of evolutionary trees, and of functional associations between gene families, as well as for the quantification of various processes guiding genome evolution. Here we describe the mathematical formalism for phylogenetic birth-and-death models. We also present an algorithm for computing the likelihood in a gain-loss-duplication model.

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