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

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