BADGER

Bayesian Analysis to Describe Genomic Evolution by Rearrangement

Version 1.02 beta, June 11, 2004

Groups

The user may partition the input taxa into groups. Each group will be maintained in all proposed phylogenies, i.e., each group will comprise the leaves of a subtree in any proposed tree. Groups are specified by using the run control group-list and by setting the run control use-groups to be true.

Each group is denoted by a positive integer. A comma-separated list gives the groups of the taxa in order, e.g., 1,2,3,1,3 means that the first taxon is in group 1, the second in 2, the third in 3, the fourth in 1, and the fifth taxon is in group 3.

A repeat count is indicated by a caret (^). For example, 1^20,2^5,3^2 means that the first twenty taxa are in group 1, the next five taxa are in 2, and the next two taxa are in group 3.

Parentheses may be used to group taxa together with a common repeat count, i.e., (1,2)^5 is the same as 1,2,1,2,1,2,1,2,1,2. Repeat counts may be nested, e.g., (1^3,2)^2 is the same as 1,1,1,2,1,1,1,2.

Repetition to the end of the list of taxa is indicated by an asterisk (*). For example, 1^5,2* means that the first five taxa are in group 1, and all the remaining taxa are in group 2. Parentheses may also be used in conjunction with the asterisk, e.g., (1,2)* is the same as 1,2,1,2,1,2,.... The group list may contain at most one asterisk and it must be associated with the last group or parenthesized groups in the list. In other words, an asterisk may appear only at the end of the list.

Examples:

• The taxa are divided over three phyla. The first phyla is composed of the first fifteen taxa, the next by the next ten taxa, and the last by six taxa.

  1^15,2^10,3^6

• The same as the above example, except that the last phyla consists of all the remaining taxa.

  1^15,2^10,3*

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