Bioinformatics Vol. 19 no. 2 2003
Pages 301-302
© 2003 Oxford University Press
Applications Note |
r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, CA 95616, USA
Received on August 2, 2002
; revised on August 29, 2002
; accepted on September 3, 2002
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{at}ucdavis.edu
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J. Pons and A. P. Vogler Complex Pattern of Coalescence and Fast Evolution of a Mitochondrial rRNA Pseudogene in a Recent Radiation of Tiger Beetles Mol. Biol. Evol., April 1, 2005; 22(4): 991 - 1000. [Abstract] [Full Text] [PDF]
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J. E. Blair and S. B. Hedges Molecular Clocks Do Not Support the Cambrian Explosion Mol. Biol. Evol., March 1, 2005; 22(3): 387 - 390. [Abstract] [Full Text] [PDF]
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A. Stamatakis, T. Ludwig, and H. Meier RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees Bioinformatics, February 15, 2005; 21(4): 456 - 463. [Abstract] [Full Text] [PDF]
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 D. J. McGeoch, D. Gatherer, and A. Dolan On phylogenetic relationships among major lineages of the Gammaherpesvirinae J. Gen. Virol., February 1, 2005; 86(2): 307 - 316. [Abstract] [Full Text] [PDF]
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C. D. Bell and M. J. Donoghue Dating the Dipsacales: comparing models, genes, and evolutionary implications Am. J. Botany, February 1, 2005; 92(2): 284 - 296. [Abstract] [Full Text] [PDF]
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D. J. McGeoch and D. Gatherer Integrating Reptilian Herpesviruses into the Family Herpesviridae J. Virol., January 15, 2005; 79(2): 725 - 731. [Abstract] [Full Text] [PDF]
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Y. Cho, J. P. Mower, Y.-L. Qiu, and J. D. Palmer From the Cover: Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants PNAS, December 21, 2004; 101(51): 17741 - 17746. [Abstract] [Full Text] [PDF]
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C. Guillet-Claude, N. Isabel, B. Pelgas, and J. Bousquet The Evolutionary Implications of knox-I Gene Duplications in Conifers: Correlated Evidence from Phylogeny, Gene Mapping, and Analysis of Functional Divergence Mol. Biol. Evol., December 1, 2004; 21(12): 2232 - 2245. [Abstract] [Full Text] [PDF]
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K. M. Pryer, E. Schuettpelz, P. G. Wolf, H. Schneider, A. R. Smith, and R. Cranfill Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences Am. J. Botany, September 1, 2004; 91(10): 1582 - 1598. [Abstract] [Full Text] [PDF]
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C. Roos, J. Schmitz, and H. Zischler Primate jumping genes elucidate strepsirrhine phylogeny PNAS, July 20, 2004; 101(29): 10650 - 10654. [Abstract] [Full Text] [PDF]
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T.-K. Seo, H. Kishino, and J. L. Thorne Estimating Absolute Rates of Synonymous and Nonsynonymous Nucleotide Substitution in Order to Characterize Natural Selection and Date Species Divergences Mol. Biol. Evol., July 1, 2004; 21(7): 1201 - 1213. [Abstract] [Full Text] [PDF]
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