4:00 pm Monday, September 16, 2013
Colloquium: From Gene Trees to Species Trees by Tandy Warnow (UT Austin) in RLM 6.104
Estimating the Tree of Life will likely involve a two-step procedure, where in the first step trees are estimated on many genes, and then the gene trees are combined into a tree on all the taxa. There are many intriguing and difficult computational problems involved in the species tree estimation. For example, even if the gene trees are correctly estimated, finding the true compatibility tree that contains all the species is NP-hard. However, estimated gene trees may not be correct, making the estimation problem additionally challenging. Finally, the true gene trees may not agree with each other or with the species tree, due to biological processes such as deep coalescence, gene duplication and loss, and horizontal gene transfer. In this talk, I will present new algorithms for these problems. We focus on the case where the gene trees can differ from the species tree due to incomplete lineage sorting. For this problem we present algorithms for the MDC (minimize deep coalescence) problem, taking gene tree estimation error into account (Yu et al., RECOMB and J Comp Biol 2011, Bayzid et al., J Comp Biol 2012). We also explore the use of "bin-and-conquer" to improve the accuracy and/or scalability of coalescent-based species tree methods (Bayzid and Warnow, Bioinformatics 2013). Submitted by
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