treeGen - Enumerate rooted tree topologies, subject to constraints
on
Enumerate rooted tree topologies, subject to constraints on
monophyletic groups. An outgroup is assumed to be specified.
treeGen spec1,spec2,spec3,... [group1,group2,...] > outfile
OR
- treeGen '*speciesFile' ['*groupFile'] > outfile
- (where speciesFile/groupFile contain whitespace-delimited names) The last
species listed is assumed to be the outgroup.
- The optional "groups" classification can be used to define
monophyletic groups. Each species may be assigned a nonnegative integer
indicating its group, with 0 indicating no group assignment. The integers
should appear in the same order as the species names. For example,
- treeGen human,chimp,macaque,mouse,rat,dog,horse,fugu 1,1,1,2,2,0,0,0
- could be used to generate all topologies of the specified vertebrate
species such that the primates (human, chimp, and macaque) and the rodents
(mouse and rat) appear as monophyletic groups. The outgroup should always
be assigned a group of 0 (a nonzero value will be ignored).
--help, -h
- Print this help message.