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

Research output: Contribution to journalArticle

1128 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)301-302
Number of pages2
JournalBioinformatics
Volume19
Issue number2
DOIs
StatePublished - Feb 1 2003
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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