PhyloGen

PhyloGen: Phylogenetic Tree Simulator Package.
Version 1.1

© Copyright 2002
Andrew Rambaut

Supported by The Royal Society and
The Wellcome Trust

Department of Zoology,
University of Oxford,
South Parks Road,
Oxford OX1 3PS, U.K.

Introduction

This package is intended to replace my Macintosh application Bi-De. It implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages or produce trees containing a random sample of lineages. Trees can be written to a file for analysis in other packages.

At present 2 models are implemented:

  • A simple birth-death process with a constant, per-lineage birth rate and death rate.
  • An episodic model which allows multiple episodes of evolution and mass exinctions.

Compilation on and running on UNIX

Details for compiling and running PhyloGen on UNIX and Linux machines are given in a file called 'Readme' which is in the UNIX distribution.

Running on Macintosh

The Apple Macintosh version of PhyloGen is available from the website.

Once PhyloGen starts to run, a command window will appear into which commands can be typed and output will be displayed. Operation of PhyloGen is then pretty much the same as the UNIX version. 

Operating PhyloGen

PhyloGen is operated by typing commands at the prompt. A command is followed on the same line by an optional number of subcommands which consist of a label and a value seperated by an '=' sign. For example:
generate replicates=1000

This command 'generate' tells PhyloGen to generate trees under the current model. The extra 'replicates=1000' subcommand asks it to produce 1000 trees (it would otherwise default to producing 1). Commands and subcommands are case insensitive an can be shortened as such that they are still unambiguous (for example "gen rep=1000").

A list of commands and their options is available here.

The usual list of commands will be something like:

birthdeath birth=0.2 death=0.1 extant=100
generate replicates=1000
sample number=100
writephylogenies file=sample.trees source=sample

This will set up a birth-death model with a birth rate of 0.2, a death rate of 0.1 with 100 extant lineages required. It will then generate 1000 phylogenies under this model. Next it will take each of these trees and produce a tree consisting of a random sample of 100 extant tips. Finally it will write the trees to a file called 'sample.trees'.

Here is an example of using the episodic growth model with two periods of growth interspersed by a mass extinction:

episodic
addgrowth birth=0.2 death=0.1 extant=1000
addextinction fraction=0.1
addgrowth birth=0.2 death=0.1 extant=1000
generate replicates=100
sample number=100
writephylogenies file=episodic.trees source=reconst

Graphical output

A couple of the commands "DRAWLTT" and "DRAWBALANCE" produce graphics in SVG format as a file on disk. SVG fomat is a cross-platform, web-based graphics format devised by Adobe and now a WWW standard. It produces high-quality editable vector-bases images that are publication quality. A free web browser plug-in to view (zoom and print) SVG files is available from the Adobe SVG web site for Macintosh, Linux and Windows. Adobe Illustrator 10.0 and Corel Draw 10.0 can both read SVG format.

Version History

Version 1.1 - December 2002

Some bug fixes and changes to the commands.

First release version 1.0 - April 2002

This is the first version and will contain bugs and all sorts of problems. Please be careful and check your results.