SYNOPSIS

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.

URL

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