PhyloGen Help
PhyloGen v1.1, ©2002 Andrew Rambaut
Department of Zoology, University of Oxford, Oxford, UK
Website: <http://evolve.zoo.ox.ac.uk>
Email: andrew.rambaut@zoo.ox.ac.uk
Please report any bugs or suggestions to the author.
Model specification commands:
- BIRTHDEATHMODEL
- Specify birth-death model and parameters
- EPISODICMODEL
- Specify episodic model and parameters
- ADDGROWTH
- Add an episode of growth to the episodic model
- ADDCONSTANT
- Add an episode of constant size to the episodic model
- ADDEXTINCTION
- Add a mass extinction to the episodic model
- CLEAREPISODES
- Clear currently set episodes from episodic model
Operation commands:
- GENERATE
- Generate phylogenies under the current model
- RECONSTRUCT
- Reconstruct trees of extant taxa only
- SAMPLE
- Sample generated phylogenies
- STATUS
- Get current simulator status
- SHAPE
- Get various statistics about the shape of the phylogenies
- WRITEPHYLOGENIES
- Write phylogenies to file
- DRAWLTT
- Draw lineages-through-time plot
General commands:
- LOG
- Log output to file
- HELP
- Use HELP <command> to get help on a command
- QUIT
- Quit the application
BIRTHDEATHMODEL
Specify birth-death phylogeny generation model.
Subcommands:
- BIRTHRATE = <real>
- Per lineage birth rate (default: 1.0)
- DEATHRATE = <real>
- Per lineage death rate (default: 0.0)
- EXTANTSTOP = <integer>
- Stop when number of extant reaches value (default: 100)
- TIMESTOP = <real>
- Stop when time reaches value (0 for no stop time) (default: 0.0)
EPISODICMODEL
Specify episodic phylogeny generation model. Episodes are added using the ADDGROWTH, ADDCONSTANT, ADDEXTINCTION commands. A growth episode should probably be the first episode.
Subcommands:
ADDGROWTH
Add an episode of growth to the simulation.
Subcommands:
- BIRTHRATE = <real>
- Per lineage birth rate (default: 1.0)
- DEATHRATE = <real>
- Per lineage death rate (default: 0.0)
- EXTANTSTOP = <integer>
- Stop when number of extant reaches value (default: 100)
- BYEXTANTSTOP = <integer>
- Stop when number of extant changes by value. Used as alternative to EXTANTSTOP. Will stop when number of extant lineages drops by specied value. (default: off)
- TIMESTOP = <real>
- Stop when time reaches value (0 for no stop time) (default: off)
- BYTIMESTOP = <real>
- Stop when time changes by value. Used as alternative to TIMESTOP. (default: off)
- MULTIPLELASTTIME = <real>
- Stop when time changes by the given multiple of previous episode's running time. Used as alternative to TIMESTOP. (default: off)
ADDCONSTANT
Add an episode of constant size to the simulation.
Subcommands:
- STOCHASTIC = TRUE | FALSE
- Stochastic fluctuation? (default: FALSE)
- RATE = <real>
- Per lineage birth/death rate (default: 1.0)
- EXTANTSTOP = <integer>
- Stop when number of extant reaches value. This can only be usedwith the stochcastic mode. (default: off)
- BYEXTANTSTOP = <integer>
- Stop when number of extant changes by value. This can only be usedwith the stochcastic mode. (default: off)
- TIMESTOP = <real>
- Stop when time reaches value (0 for no stop time) (default: off)
- BYTIMESTOP = <real>
- Stop when time changes by value. Used as alternative to TIMESTOP. (default: off)
- MULTIPLELASTTIME = <real>
- Stop when time changes by the given multiple of previous episode's running time. Used as alternative to TIMESTOP. (default: 1.0)
ADDEXTINCTION
Add a mass extinction to the simulation.
Subcommands:
- FRACTION = <real>
- Fraction of extant lineages to go extinct (default: 0.5)
- NUMBER = <integer>
- Number of extant lineages to go extinct (default: off)
- PROBABILITY = <real>
- Per lineage probability of extant lineages going extinct (default: off)
CLEAREPISODES
Clear currently set episodes from episodic model.
GENERATE
Generate trees under the current model.
Subcommands:
- REPLICATES = <integer>
- Number of phylogenies to generate (default: 1)
- ATTEMPTS = <integer>
- Number of attempts to make in cases of all lineages going extinct. (default: 1000 times number of trees to generate)
- RECONSTRUCT = TRUE | FALSE
- Create reconstructed phylogenies (extant lineages only)? (default: true)
- KEEP = TRUE | FALSE
- Keep whole phylogenies after reconstructing? (default: true)
RECONSTRUCT
Reconstruct trees of extant taxa only.
Subcommands:
- KEEP = TRUE | FALSE
- Keep whole phylogenies list after reconstructing? (default: TRUE)
SAMPLE
Specify sampling conditions.
Subcommands:
- REPLICATES = <integer>
- Number of samples to make of each phylogeny in list (default: 1)
- SOURCE = WHOLE | RECONSTRUCTED
- Sample from the whole phylogenies or reconstructed (default: RECONSTRUCTED)
- KEEPSOURCE = TRUE | FALSE
- Keep source phylogenies list after sampling (default: TRUE)
- FRACTION = <real>
- Fraction of tips to sample (default: 0.5)
- NUMBER = <integer>
- Number of tips to sample (default: off)
- PROBABILITY = <real>
- Per tip probability of sampling (default: off)
STATUS
Get current simulator status.
Subcommands:
- MEMORY = <boolean>
- Report information about memory use (default: off)
SHAPE
Get various statistics about the shape of the phylogenies.
Subcommands:
- SOURCE = <WHOLE | RECONSTRUCTED | SAMPLED>
- Analyse the whole, reconstructed, or sampled trees. (default: RECONSTRUCTED)
WRITEPHYLOGENIES
Write phylogenies to a file.
Subcommands:
- FILE = <file name>
- Name of file (default: 'whole.tf' | 'reconstructed.tf' | 'sampled.tf)
- FORMAT = <PHYLIP | NEXUS>
- Format of file to write. (default: PHYLIP)
- SOURCE = <WHOLE | RECONSTRUCTED | SAMPLED>
- Write the whole, reconstructed, or sampled trees. (default: RECONSTRUCTED)
DRAWLTT
Draw lineages-through-time plot. For some versions, write to file must be used.
Subcommands:
- FILE | FILE = <file name>
- Write to file ('ltt.svg') or specify name of file to write
- PHYLOGENY = <integer>
- Which phylogeny to draw (default: 1)
- WHOLE = <boolean>
- Draw LTT for whole phylogeny (default: true)
- RECONSTRUCTED = <boolean>
- Draw LTT for reconstructed phylogeny (default: true)
- SAMPLED = <boolean>
- Draw LTT for sampled phylogeny, if available (default: true)
- TOLERANCE = <real>
- Minimum time between points to draw (for very large phylogenies) (default: 0.0)