r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

Michael J Sanderson

doi:10.1093/bioinformatics/19.2.301

r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock

Bioinformatics. 2003 Jan 22;19(2):301-2. doi: 10.1093/bioinformatics/19.2.301.

Author

Michael J Sanderson¹

Affiliation

¹ Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, CA 95616, USA. mjsanderson@ucdavis.edu

PMID: 12538260
DOI: 10.1093/bioinformatics/19.2.301

Abstract

Summary: Estimating divergence times and rates of substitution from sequence data is plagued by the problem of rate variation between lineages. R8s version 1.5 is a program which uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. Unlike most programs for rate inference or phylogenetics, r8s permits users to convert results to absolute rates and ages by constraining one or more node times to be fixed, minimum or maximum ages (using fossil or other evidence). Version 1.5 uses truncated Newton nonlinear optimization code with bound constraints, offering superior performance over previous versions.

Availability: The linux executable, C source code, sample data sets and user manual are available free at http://ginger.ucdavis.edu/r8s.

MeSH terms

Algorithms*
Database Management Systems*
Databases, Genetic
Evolution, Molecular*
Genetic Drift
Genetic Variation / genetics*
Phylogeny*
Sequence Analysis, DNA*
Software
Time Factors