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.
Recent
papers using GeneTree
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Page, R.D.M. and J Cotton (in press). Vertebrate phylogenomics: reconciled trees and gene duplications. PSB 2002. |
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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. |
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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.
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Page, R. D. M. (1998). GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics, 14:819-820. [MEDLINE record] |
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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. |
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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)
Download the Power Macintosh version
The Mac
OS version of GeneTree requires a font called "COMPONENTMonaco." To use this
font, drop the "COMPONENT Font File" onto your System folder.
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.