pkgsrc-wip/r8s/DESCR

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This is a program for estimating 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.