Provided by: prime-phylo_1.0.11-4build2_amd64
primeGEM - Guest-in-host tree reconciliation tool
primeGEM [OPTIONS] guest-tree species-tree [gene-species-map]
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.
-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.
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The prime-phylo home page: http://prime.sbc.su.se
primeDTLSR(1), primeDLRS(1), showtree(1), chainsaw(1), reconcile(1), reroot(1), tree2leafnames(1), treesize(1)