Disk covering methods improve phylogenomic analyses

BMC Genomics

Research

Tyler Hunt¹  Md Shamsuzzoha Bayzid¹  Tandy Warnow² 

[1] Department of Computer Science, University of Texas at Austin, 78712, Austin, TX, USA;Department of Computer Science, University of Texas at Austin, 78712, Austin, TX, USA;Department of Bioengineering, The University of Illinois, 61801, Urbana, Champaign, USA;

关键词: multi-species coalescent process;    incomplete lineage sorting;    MP-EST;    disk covering methods;    divide-and-conquer;   

DOI  :  10.1186/1471-2164-15-S6-S7

来源: Springer

【 摘 要 】

MotivationWith the rapid growth rate of newly sequenced genomes, species tree inference from multiple genes has become a basic bioinformatics task in comparative and evolutionary biology. However, accurate species tree estimation is difficult in the presence of gene tree discordance, which is often due to incomplete lineage sorting (ILS), modelled by the multi-species coalescent. Several highly accurate coalescent-based species tree estimation methods have been developed over the last decade, including MP-EST. However, the running time for MP-EST increases rapidly as the number of species grows.ResultsWe present divide-and-conquer techniques that improve the scalability of MP-EST so that it can run efficiently on large datasets. Surprisingly, this technique also improves the accuracy of species trees estimated by MP-EST, as our study shows on a collection of simulated and biological datasets.

【 授权许可】

CC BY   
© Bayzid et al.; licensee BioMed Central Ltd. 2014