primeGEM - Guest-in-host tree reconciliation tool

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.

0      Successful program execution.

       1      Some error occurred

       primeGEM - Guest-in-host tree reconciliation tool

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

       -oFILE
              Output filename.

       -iINT Number of iterations.

       -tINT Thinning

       -m     Do maximum likelihood. No MCMC.

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

       -sINT 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)

       -BfFLOATFLOAT
              Fix the birth/death rates to these values

       -BpFLOATFLOAT
              start values of birth/death rate parameters

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

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

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

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

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

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