NAME

       primeGEM - Guest-in-host tree reconciliation tool

SYNOPSIS

       primeGEM [OPTIONS] guest-tree species-tree [gene-species-map]

DESCRIPTION

       guest-tree Name of file containing guest tree.

       species-tree Species tree in Newick format. with divergence times.

       gene-species-map  A  file  that  contains  lines  with a gene name in the first column and
       species name as found in the species tree in the  second. You can also choose to associate
       the genes with species in the gene tree.

OPTIONS

       -h, -u Display help (this text).

       -o FILE
              Output filename.

       -i INT Number of iterations.

       -t INT Thinning

       -m     Do maximum likelihood. No MCMC.

       -w INT Write to stderr INT times less often than to stdout.

       -s INT Seed  for  pseudo-random number generator. If set to 0 (default), the process id is
              used as seed.

       -q     Do not output diagnostics to stderr.

       -g     Debug info.

       -l     Output likelihood. No MCMC.

       -Gr    reroot gene tree. Default is a fixed root.

       -Go    Estimate orthology. Default is discard orthology data.

       -Gs    record speciation probabilities (orthology probabilities will not be recorded)

       -Bf FLOAT FLOAT
              Fix the birth/death rates to these values

       -Bp FLOAT FLOAT
              start values of birth/death rate parameters

       -Bt FLOAT
              fix 'top time', the time between the first duplication  and  root  of  S,  to  this
              value.

       -Bb FLOAT
              The beta parameter for a prior distribution on species root distance.

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),   showtree(1),   chainsaw(1),   reconcile(1),   reroot(1),
       tree2leafnames(1), treesize(1)