3 commits

Author	SHA1	Message	Date
Roland Illig	1ee539a984	Added RMD160 checksums.	2005-09-28 06:41:05 +00:00
David	b7c9f9fecf	updated to reflect new patch aa and ab	2005-03-18 20:02:03 +00:00
David	213af65342	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.	2005-01-16 18:54:25 +00:00