NAME

       reconcile - This program outputs the reconciliation that minimizes the number of duplications

SYNOPSIS

       reconcile [OPTIONS] gene-tree species-tree [gene-species-map]

DESCRIPTION

       This program outputs the reconciliation that minimizes the number of duplications

OPTIONS

       --help Display help (this text).

       -V, --version
              Print version and exit

       -r, --reroot any|random|no
              Reroot  the  tree  to  minimize the number of implied duplications/losses if the most parsimonious
              reconciliation is chosen. Default is "no".

       -w --weights FLOAT FLOAT
              Determine the relative importance of duplications vs losses. First weight is for duplications  and
              the second for losses. The default is 1.0,0.0 which counts duplications only. Weights are required
              to be positive.

EXIT STATUS

       0      Successful program execution.

       1      Some error occurred

URL

       The prime-phylo home page: http://prime.sbc.su.se

SEE ALSO

       primeDTLSR(1),   primeDLRS(1),  primeGEM(1),  chainsaw(1),  reconcile(1),  reroot(1),  tree2leafnames(1),
       treesize(1)

prime-phylo 1.0.11                                13 Mar, 2012                                      reconcile(1)