NAME

       treeGen - Enumerate rooted tree topologies, subject to constraints on

DESCRIPTION

       Enumerate  rooted tree topologies, subject to constraints on monophyletic groups.  An outgroup is assumed
       to be specified.

SYNOPSIS

       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).

OPTIONS

       --help, -h

              Print this help message.