2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2019

Dominik Schrempf, Bui Quang Minh, Nicola {De Maio}, Arndt {von Haeseler}, Carolin Kosiol. Reversible polymorphism-aware phylogenetic models and their application to treeinference. Journal of theoretical biology, 407:362-370. 2016.

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We present a reversible Polymorphism-Aware Phylogenetic Model (revPoMo) for
species tree estimation from genome-wide data. revPoMo enables the reconstruction
of large scale species trees for many within-species samples. It expands the
alphabet of DNA substitution models to include polymorphic states, thereby,
naturally accounting for incomplete lineage sorting. We implemented revPoMo in
the maximum likelihood software IQ-TREE. A simulation study and an application to
great apes data show that the runtimes of our approach and standard substitution 
models are comparable but that revPoMo has much better accuracy in estimating
trees, divergence times and mutation rates. The advantage of revPoMo is that an
increase of sample size per species improves estimations but does not increase
runtime. Therefore, revPoMo is a valuable tool with several applications, from
speciation dating to species tree reconstruction.