TreeMaker

Background

Biodiversity assessment demands objective measures, because ultimately conservation is an issue of economics, prioritizing the use of limited resources for preserving taxa. The most general framework for such metrics are those that assess evolutionary distinctiveness as judged by how much of a phylogeny is conserved. However, their applicability is limited by the still small proportion of taxa that have been reliably placed in a phylogeny. Given that this is unlikely to be corrected soon, alternatives are needed. Taxonomy can be used as a reasonable surrogate for phylogeny. Combining this with searches for combinations of local sites containing maximal diversity, the efficacy of any conservation schemes can be determined from a taxonomy of the organisms involved and the abundance data at potential preservation sites.

To this end, TreeMaker is software that allows the interactive building and editing of a taxonomy and its conversion into a phylogeny for the above calculations. It also allows the editing of site abundance and species richness data. This data may be imported from and exported to a variety of formats for interoperability with other programs. While it is mainly intended for use in conservation and biodiversity, it can be used as a simple tool for building phylogenies.

TreeMaker was written in RealBasic and developed under MacOSX. It was produced with the help of Ross Crozier and Lisa Dunnett of James Cook University, Australia.

If this software is used in any publication, cite:

Ross H Crozier, Lisa J Dunnett, Paul-Michael Agapow (2005). Phylogenetic biodiversity assessment based on systematic nomenclature. Evolutionary Bioinformatics Online 1:11-36.

Installation

TreeMaker is available as a standalone program for MacOS (both OSX and Carbon) and Windows. Across platforms, it has only cosmetic not functional differences. Similarly, the datafiles TreeMaker produces may be used across platform. There are no special memory or library requirements. TreeMaker may be installed by simply copying it to an appropriate place on a local hardisk. To use the online help from within TreeMaker, the HTML manual file must be in the same directory as the application. Several associated programs (like MeSA and Conserve) can be found on this site.

Usage

A full manual is included with the distribution.

Limitations

None.

References

• Lisa Dunnett has also produced a program called TreeMaker with roughly equivalent functionality. It used to be found at http://homes.jcu.edu.au/~jc125033/Treemaker.htm.