GeneTree icontitle

A program for comparing gene and species trees

GeneTree is an experimental program for comparing gene and species trees. Currently it is available for Mac OS (System 7.5 or later running on a PowerMac), and Windows 95/NT 4.0 or later. If you download the program please join the mailing list so you can be kept informed of new releases and bug fixes.

Your e-mail address:

Recent papers using GeneTree

Get preprint Page, R.D.M. and J Cotton (in press). Vertebrate phylogenomics: reconciled trees and gene duplications. PSB 2002.
Get preprint Page, R.D.M. and Cotton, J.C. (2000) GeneTree: a tool for exploring gene family evolution. In D. Sankoff, and J. Nadeau, (eds.), Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families. Kluwer Academic Publishers, Dordrecht, pp. 525-536.
Get preprint Page, R. D. M. (2000). Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Molecular Phylogenetics and Evolution, 14:89-106. [MEDLINE record] [Data sets]

Background reading

If you are interested in using GeneTree I strongly suggest that you read the following papers which outline the concepts behind the program. Preprints of these papers can be downloaded from this site.

PDF Page, R. D. M. (1998). GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics, 14:819-820. [MEDLINE record]
PDF Page, R. D. M. and Charleston, M. A. (1997a). From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution, 7, 231-240.
PDF Page, R. D. M. and Charleston, M. A. (1997b). Reconciled trees and incongruent gene and species trees. In: B. Mirkin, F. R. McMorris, F. S. Roberts and A. Rzhetsky (eds), Mathematical hierarchies in biology , Vol. 37, American Mathematical Society.

There are also some technical papers by mathematicians interested in reconciled trees available here.

Downloading and installing the software

Current release is 1.3.0 (4 October 2001)

.sea icon Download the Power Macintosh version

font The Mac OS version of GeneTree requires a font called "COMPONENTMonaco." To use this font, drop the "COMPONENT Font File" onto your System folder.

.zip icon Download the Win 95/NT 4.0 version


Previous releases

1.1.1 (7 August 2000)

Extract the ZIP file and run the program SETUP.EXE to install the program. You can delete GeneTree using the Add/Remove Programs control panel.



A draft manual for GeneTree is available online as an Adobe Acrobat PDF file.

This page last updated 4 October 2001.