Software and manuals
Software and manuals
Bayesian dating step-by-step manual (version 1.5, July 2005)
Based on manuals and readme files by Jeff Thorne and Ziheng Yang, I compiled a step-by-step manual on Bayesian molecular dating using PAML and multidivtime.
The step-by-step manual is nothing else than a compilation of the original manuals and readme files by Jeff Thorne and Ziheng Yang. It describes how to perform a Bayesian molecular dating using the software PAML and multidivtime. The manual assumes that you already have one or more DNA sequence matrices and a corresponding phylogenetic tree topology.
The Bayesian molecular dating method by Thorne et al. (1998) and Kishino et al. (2001) uses a probabilistic model to describe the change in evolutionary rate over time and uses the Markov chain Monte Carlo (MCMC) procedure to derive the posterior distribution of rates and times. It allows simultaneous use of different substitution models for multiple data partitions as well as multiple calibration windows, and provides direct credibility intervals for estimated divergence times and substitution rates.
Download the manual as pdf (110 KB), or visit the official multidivtime website.
RATO: Extract ratograms from the multidivtime dating output (version 1.3, December 2005)
RATO is a Perl utility by Torsten Eriksson and myself to extract a ratogram from the main multidivtime output file. Additionally, it calculates the average rate of all branches and writes it together with the ratogram into a NEXUS treefile. Such a file can be read by programs like PAUP* or TreeView, from where the ratogram can be printed.
Since version 1.3, RATO is able to extract the rates from multiple genes. In such a case, multiple ratograms (one per gene) will be written to the output file. Additionally, RATO calculates the average rate for each branch across all genes, and adds an "averaged ratogram" to the output file. This final ratogram contains therefore rates averaged over all genes.
Download RATO as zip archive (5 KB).
RATO requires an installed Perl distribution on your computer. You can download Perl for free as a source code or as a pre-compiled binary distribution at http://www.perl.com/download.csp.