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.