BAMBE

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.

Category lists

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

Parentheses may be used to group sites 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 sites is indicated by an asterisk (*). For example, 1^5,2* means that the first five sites are in category 1, and all the remaining sites are in category 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 category list may contain at most one asterisk and it must be associated with the last category or group in the list. In other words, an asterisk may appear only at the end of the list.

Examples:

• All sites are the same category.

  1*

• All sites are partitioned by codon position.

  (1,2,3)*

• The sites are divided over three genes. Each gene has its own set of parameters used by all sites in that gene. The first gene is composed of the first ninety-nine sites, the next by the next fifty sites, and the last by nine sites.

  1^99,2^50,3^9

• The same as the above example, except that the first and third gene are partitioned by codon position but use the same parameters. The second gene has its own set of parameters used by all sites in that gene.

  (1,2,3)^33,4^50,(1,2,3)^3

• The same as the above example, but the first and third gene use different parameters.

  (1,2,3)^33,4^50,(5,6,7)^3

• The same as the previous example, except that the first gene is composed of 101 sites.

  (1,2,3)^33,1,2,4^50,(5,6,7)^3

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