Bioinformatics Vol. 16 no. 4 2000
Pages 395-399
© 2000 Oxford University Press
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
1 Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, , UK
Received on November 29, 1999
; revised on March 7, 2000
; accepted on March 7, 2000
Motivation: TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated date of the most recent common ancestor of the sequences, under a model which assumes a constant rate of substitution (molecular clock) but which accommodates the dates of isolation. Confidence intervals for these parameters are also estimated.
Results: The approach was applied to a sample of 17 dengue virus serotype 4 sequences, isolated at dates ranging from 1956 to 1994. The rate of substitution for this serotype was estimated to be 7.91 x 10-4 substitutions per site per year (95% confidence intervals of 6.07 x 10-4, 9.86 x 10-4). This is compatible with a date of 1922 (95% confidence intervals of 1900–1936) for the most recent common ancestor of these sequences.
Availability: TipDate can be obtained by WWW from http://evolve.zoo.ox.ac.uk/software. The package includes the source code, manual and example files. Both UNIX and Apple Macintosh versions are available from the same site.
Contact: andrew.rambaut{at}zoo.ox.ac.uk
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