CVS commit: wip/r8s

[David <daprice%users.sourceforge.net@localhost>]

Module name:    pkgsrc-wip
Committed by:   daprice
Date:           Wed Feb 23 19:01:30 UTC 2005

Import into wip/r8s

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. 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.

Status:

Vendor Tag:     daprice
Release Tags:   daprice_20050223
                
U wip/r8s/Makefile
U wip/r8s/DESCR
U wip/r8s/distinfo
U wip/r8s/PLIST
U wip/r8s/patches/patch-aa
U wip/r8s/patches/patch-ab

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