Molecular Evolution Activities
 

This is a comprehensive bibliography (under construction) of primary and secondary sources on the neutral theory of molecular evolution. It currently covers the period 1973-2001.

Author :

Rambaut, A.

Year :

2000

Title :

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

Journal :

Bioinformatics

Volume :

16

Issue :

4

Pages :

395-9

Short Title :

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum

Custom 3 :

20328052

Abstract :

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.
 -- contributed by John Beatty, March 29, 2002