Work

Fast and Slow Implementations of Relaxed-Clock Methods Show Similar Patterns of Accuracy in Estimating Divergence Times

Year: 2011

Type: article

Abstract: Phylogenetic analyses are using increasingly larger data sets for estimating divergence times. With this increase in data sizes, the computation time required is becoming a bottleneck in evolutionary investigations. Our recent study of two relaxed-clock programs (BEAST and MultiDivTime [MDT]) showed their usefulness in time estimation; however, they place a significant computational time burden on biologists even for moderately small data sets. Here, we report speed and accuracy of another relaxed-clock program (MCMCTree, MC2T). We find it to be much faster than both MDT and BEAST while producing comparable time estimates. These results will encourage the analysis of larger data sets as well as the evaluation of the robustness of estimated times to changes in the model of evolutionary rates and clock calibrations.

Source: Molecular Biology and Evolution

DOI: 10.1093/molbev/msr100

Authors: Fabia U. Battistuzzi, Paul Billing-Ross, Aditya Paliwal, Sudhir Kumar

Institution: Arizona State University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Science Foundation, Howard Hughes Medical Institute, Arizona State University, National Human Genome Research Institute

Awards: G4364466792, Bioinformatics of Molecular Timetrees, Comparative Molecular Sequence Analysis