2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2016

Siavash Mirarab, Md Shamsuzzoha Bayzid, Bastien Boussau, Tandy Warnow. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science, 346(6215):1250463. 2014.

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Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce
the accuracy of concatenation-based estimations of species trees. Although
coalescent-based species tree estimation methods can have good accuracy in the
presence of ILS, they are sensitive to gene tree estimation error. We propose a
pipeline that uses bootstrapping to evaluate whether two genes are likely to have
the same tree, then it groups genes into sets using a graph-theoretic
optimization and estimates a tree on each subset using concatenation, and finally
produces an estimated species tree from these trees using the preferred
coalescent-based method. Statistical binning improves the accuracy of MP-EST, a
popular coalescent-based method, and we use it to produce the first genome-scale 
coalescent-based avian tree of life.