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

Each category has its own set of parameters. Each category is denoted by a positive integer between 1 and 10. A comma-separated list gives the categories of the sites in order, e.g., 1,2,3,1,3 means that the first site is in category 1, the second in 2, the third in 3, the fourth in 1, and the fifth site is in category 3.

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:


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

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