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)