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

Research output: Contribution to journalArticle

1083 Citations (Scopus)

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

Fingerprint

Molecular Evolution
Clocks
Divergence
Substitution reactions
Semiparametric Methods
Bound Constraints
Nonparametric Methods
Phylogenetics
Nonlinear Optimization
Rate Constant
Convert
Substitution
Vertex of a graph
Estimate

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

r8s : Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. / Sanderson, Michael.

In: Bioinformatics, Vol. 19, No. 2, 01.02.2003, p. 301-302.

Research output: Contribution to journalArticle

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