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.