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)