Log Message:
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. T
 erminal 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.