BAMBE

Bayesian Analysis in Molecular Biology and Evolution

Version 2.03 beta, January 2001

Changes

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:

C++

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 branch lengths.

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.

beta.ps.

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.

Old New
initial-delta global-tune
initial-kappa-delta kappa-tune
theta-const theta-tune
pi-const pi-tune
N/A local-tune
N/A ttp-tune
N/A gamma-tune
N/A beta-tune
N/A initial-tree-type
N/A use-beta
N/A update-ttp
N/A update-gamma

Update parameters when running TN93

Old	New
initial-delta	global-tune
initial-kappa-delta	kappa-tune
theta-const	theta-tune
pi-const	pi-tune
N/A	local-tune
N/A	ttp-tune
N/A	gamma-tune
N/A	beta-tune
N/A	initial-tree-type
N/A	use-beta
N/A	update-ttp
N/A	update-gamma

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.

Back to the table of contents.

This page was most recently updated on January 19, 2001.

bambe@mathcs.duq.edu