Here are several computer programs that estimate divergence times. Many of these programs are designed to be used on a computer running a Unix/Linux operating system. This list is by no mean complete and in no particular order.
Jeff Thorne's DIVTIME and MULTIDIVTIME programs.
Michael Sanderson's r8s This is a program for estimating absolute rates ("r8s") of molecular evolution and divergence times on a phylogenetic tree. It implements several methods for estimating these parameters ranging from fairly standard maximum likelihood methods in the context of global or local molecular clocks to more experimental semiparametric and nonparametric methods that relax the stringency of the clock assumption using smoothing methods. Its starting point is a given phylogenetic tree and a given set of estimated branch lengths (numbers of substitutions along each branch). In addition one or more calibration points can be added to permit scaling of rates and times to real units. These calibrations can take one of two forms: assignment of a fixed age to a node, or enforcement of a minimum or maximum age constraint on a node, which is generally a better reflection of the information content of fossil evidence. Terminal nodes are permitted to occur at any point in time, allowing investigation of rate variation in phylogenies such as those obtained from 'serial' samples of viral lineages through time. Finally, it is possible to assign all divergence times (perhaps based on outside estimates of divergence times) and examine molecular rate variation under several models of smoothing. The current version of the program available in several forms; source code in a mixture of C, C++ and Fortran, with a Makefile, executable binary file for Linux (x86) machines, and executable binary file for Mac OS 10.2. The nonparametric smoothing (NPRS) methods is described in, Sanderson, M. J. 1997 (A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218-1231) and the penalized likelihood method (PL) is outlined in Sanderson, M. J. 2002 (Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology Evolution 19:101-109).
Joe Felsenstein's PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). It is available free over the Internet, and written to work on as many different kinds of computer systems as possible. The source code is distributed (in C), and for some particular systems executables are also distributed. In particular, already-compiled executables are available for Windows95/98/NT, Windows 3.x, DOS, PowerMac, and 68k Macintosh systems. Complete documentation is available on documentation files that come with the package. PHYLIP allows for the estimation of divergence times under a strict molecular clock, using a variety of models of sequence evolution.
Ziheng Yang's PAML package. This is a package of programs for the maximum likelihood analysis of nucleotide or protein sequences, including codon-based methods that take into account both amino acids and nucleotides. The package also allows analysis of a 'relaxed' molecular clock, or local clock, as described in Yoder and Yang, 2000 (Estimation of primate speciation dates using local molecular clocks. Molecular Biology and Evolution 17: 1081-1090). This method allows for different part of a tree to have different rates. The package is available as ANSI C source code for Unix systems, as PowerMac executables and as executables that run on Windows95, Windows98, and WindowsNT.
David Swofford's PAUP* Allows for the estimation of branch lengths (expected number of nucleotide substitutions/per site) under a wide variety of DNA sequence evolution models. Is available for *NIX, Mac, and PC formats from Sinauer Associates, Inc.
Andrew Rambaut's QDate, TipDate, and BEAST. QDate is an application for estimating the date of divergence between two pairs of sequences given that the date of divergence of the members of each pairs is known. QDate analyses data under three different models: a) The1-rate model in which the entire quartet is assumed to have evolved at the same rate. b) The 2-rate model in which one pair in the quartet has a different rate from the other. c) The 5-rate model in which each branch in the tree has a different rate (the standard maximum likelihood model). This latter model is used as an alternative hypothesis against which to test the first two. TipDate is an application for estimating the rate molecular evolution (and hence a time-scale) for a phylogeny consisting of dated tips. These will most frequently be from viruses or other fast-evolving pathogens that have been isolated over a range of dates. The program can also return the likelihood for the simple molecular clock model (i.e., assuming that all sequences are contemporary) or the non-clock model. These are useful for likelihood ratio tests of the fit of the model to the data. BEAST is a new cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards molecular clock analyses. It is not intended as a method of constructing phylogenies but rather testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. It uses a complex input format that allows the user to design and run a large range of models. We also include a program that can convert NEXUS files into this format.