R8s
Description
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.
License
GNU GPL v3 and proprietary,
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of r8s and load default version of r8s as
module avail r8s/ # list available modules module load r8s # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail r8s
and choose explicit version you want to use.
Documentation
http://ceiba.biosci.arizona.edu/r8s/