BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Copyright © 2004 by Bret Larget & Don Simon


Algorithms


Tree representation

The proposed phylogeny is represented by an unrooted tree. The leaves contain signed permutations representing the genome arrangements of the taxa in the data set. Internal nodes contain signed permutations representing proposed intermediate taxa. Each edge is annotated with a list of reversals that will transform the permutation in one endpoint to the permutation in the other endpoint.

Tree proposal algorithms

At present, there are eight tree proposal algorithms in BADGER, listed below. In interpreting the illustrations, please note the following:

is a node whose permutation may be changed by the update,
, are reversals,
, are new reversals, and
is a path, rather than a direct edge.

In the diagrams, a new reversal list may differ in length from the original list. Also, nodes shown with a single adjacent edge may be leaves, or may be internal nodes whose other edges are not shown.