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
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
Parentheses may be used to group taxa together with a common repeat
(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
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
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.
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