TreeSample Introduction

This package contains evolutionary models of speciation for phylogenetic trees and algorithms for sampling from these models. The initial set of algorithms available in this package corresponds to those in:

Sampling trees from evolutionary models
Klaas Hartmann, Dennis Wong, Tanja Gernhard
Systematic Biology, in press

The project consists of (i) a Perl package called Bio::Phylo::EvolutionaryModels and (ii) a GUI for this called TreeSample.

TreeSample GUI

The TreeSample GUI provides a graphical interface allowing you to sample trees from several inbuilt models or your own specified Newick trees.

Windows Installation

Windows users can download a self-contained executable from the Downloads tab. Download the executable and save it somewhere convenient (eg. your desktop). To run TreeSample simply run (double-click) this executable, it may take a little while to start.

Platform independent Installation

Users of other operating systems must install the Bio::Phylo::EvolutionaryModels package which includes TreeSample (see below). In addition to the prerequisites for Bio::Phylo::EvolutionaryModels (see below) the package wxPerl must also be installed. To run the GUI simply run TreeSample.pl (eg. run perl TreeSample.pl in the installed location)

Bio::Phylo::EvolutionaryModels

Bio::Phylo::EvolutionaryModels is a Perl package that permits you to sample phylogenetic trees from either (i) several pre-defined models of speciation or (ii) your own speciation model. Extensive documentation and examples are included in the source code.

Platform Independent Installation

Ultimately this should be a part of the Perl Bio::Phylo package and should install automatically with this. In the interim:

• Install the pre-requisites (Bio::Phylo > 0.17_RC9, Math::CDF, Perl > 5.8)
• Download the source from the downloads page or svn checkout

Related Projects

Some of the algorithms developed here are also available as: