cmd.HPTN071.input.parser.v4 | Command line generator for 'HPTN071.input.parser.v2' |
cmd.HPTN071.simulator | Command line generator for 'HPTN071.simulator' |
cmd.SeqGen.createInputFiles | Command line generator for... |
cmd.SeqGen.run | Command line generator for 'prog.PANGEA.SeqGen.run' |
cmd.VirusTreeSimulator | Command line generator for the 'VirusTreeSimulator' |
PANGEA.GTR.params | Create data.table of GTR parameters |
PANGEA.RootSeq.create.sampler | Create starting sequence sampler |
PANGEA.TransmissionEdgeEvolutionaryRate.create.sampler | Create sampler of Evolutionary Rates for transmission edges |
PANGEA.WithinHostEvolutionaryRate.create.sampler.v1 | Create sampler of Within Host Evolutionary Rates |
sim.regional | Simulate sequences and viral phylogenetic trees under the... |
sim.regional.args | Input arguments to simulate sequences and viral phylogenetic... |
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