Bayesian Analysis in Molecular Biology and Evolution
Version 2.03 beta, January 2001
© Copyright 2000, 2001, Donald Simon & Bret Larget,
Department of Mathematics and Computer Science, Duquesne University.
- New in Version 2.03b:
- Fixed a problem with const references to local strings.
- Added stdlib.h to meansd.C.
- New in Version 2.02b:
- Small changes to address numerical problems with some machines.
- New in Version 2.01b:
We have completely rewritten BAMBE in C++ to simplify porting to Windows
and Macintosh and to simplify future code maintenance.
The new code uses better memory management
and is a bit faster than the previous released version in C.
- No built-in restrictions on number of taxa or number of sites.
- Beta Distribution modification to LOCAL
We have added an optional modification to the local update
which selects branching points according to a beta distribution
with mean the current value rather than a uniform distribution.
This change allows good mixing behavior of the Markov chain
in some situations where local performed poorly, specifically in cases
where there was great disparity in the lengths of neighboring
The run setting use-beta=true turns on this option.
The tuning parameter for this option is the sum of the two beta parameters.
The default value is beta-tune=10.0.
A description of this update and details on the derivation
of the appropriate Hastings ratio is available as a PostScript file.
- Alternative initial starting trees
In addition to starting a run at a tree chosen from the prior,
users may also begin runs at the neighbor-joining or UPGMA trees
using maximum likelihood distances under any specified model.
- Changed names for some run settings
We have renamed some run settings.
Tuning parameters have the word ``tune'' as part of the name.
Run settings for the initial tree are different as well.
- Update parameters when running TN93
- The parameters gamma and ttp (transition/transversion parameter) from the Tamura-Nei 1993
model may now be updated and are not required to stay fixed.
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This page was most recently updated on January 19, 2001.