./wip/r8s, Estimate rates of molecular evolution

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Branch: CURRENT, Version: 1.70, Package name: r8s-1.70, Maintainer: brook

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.


Required to build:
[pkgtools/cwrappers]

Master sites:

RMD160: 6e5ba652fae3fe4cb0c03fb6b46e6635d8eed53c
Filesize: 1848.314 KB

Version history: (Expand)

CVS history: (Expand)


   2012-10-07 16:07:06 by Aleksej Saushev | Files touched by this commit (1) 
Log message:
Support staged installation.
   2009-10-11 12:45:10 by Thomas Klausner | Files touched by this commit (261) 
Log message:
Remove obsolete @dirrm lines.
   2007-07-15 20:33:16 by Sergey Svishchev | Files touched by this commit (7) 
Log message:
Follow redirects.
   2005-09-28 08:41:35 by Roland Illig | Files touched by this commit (132) 
Log message:
Added RMD160 checksums.
   2005-04-20 01:45:57 by David | Files touched by this commit (1) 
Log message:
changed (dollar)f to (dollar){f}
   2005-04-11 23:15:26 by Todd Vierling | Files touched by this commit (1) 
Log message:
Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.
   2005-03-31 22:47:51 by David | Files touched by this commit (1) 
Log message:
initial import of patch-ac, which adds a main to make libg2c happy
   2005-03-18 21:02:04 by David | Files touched by this commit (1) | Package updated
Log message:
updated to reflect new patch aa and ab