This is the command primeGEM that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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