r8s v1.8 (Estimate absolute rates of molecular evolution and divergence times on a phylogenetic tree)
r8s 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.
In version 1.8, ancestral state reconstruction and model testing for several markov models of morphological evolution (see below) have been added.
The program reads "NEXUS" formatted data files (Maddison et al. 1997).