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Welcome! Here you can find information and download files related the CoMET project.

What is CoMET?

CoMET stands for Continuous-character Model Evaluation and Testing and is a module for the Mesquite Project. Give it a tree topology as a starting point and some phenotypic data, CoMET tells you the likelihoods of the data evolving through nine different evolutionary models.  For additional information, please see the documentation.

Program Downloads

CoMET is licensed under the LGPL.

• CoMET program files (.zip) (September 2007)
This is the main Java class files you'll need to run CoMET.
• CoMET source code (.zip) (September 2007). These are the Java source code files for CoMET.
• CoMET runs on top of the Mesquite 2.0. Please download Mesquite from http://www.mesquiteproject.org.  CoMET includes a subset of the recent version of the PAL project. These PAL files have been repackaged into CoMET due to the differences between Mesquite's PAL and CoMET's PAL files.

Documentation / Citing CoMET

• CoMET User's Guide (.doc)

This guide contains a short description, written by Chunghau Lee, of CoMET plus installation and usage instructions. Last updated 12 February 2006.

You can also see Chunghau's MS thesis. Note Chapter 3 has some simulations of punctuated models.

 

• To cite CoMET:

C Lee, S Blay, AØ Mooers, A Singh, and TH Oakley (2006). CoMET: A Mesquite package for comparing models of continuous character evolution on phylogenies. Evolutionary Bioinformatics Online. 2:193-196. Download (pdf)

 

Release History

23 September 2007

19 August 2006

• The punctuated-maximal model has returned by popular demand. To use it, start with the tree window, then from the menu, select Analysis -> Tree Legend -> Tree value using character matrix (or just "Tree value using character", that works too). Then check the box that says "Show Secondary Choices" to see the option for "CoMET on Matrix (or Character): Punctuated Maximal Only". This module does not calculate the AIC, but it does print for you (in the logs) the maximal branch lengths with each of the models.
• Canceling the computation of "Punctuated Avg" now works. When prompted for the asymmetry ratio, just click "Cancel".
  

24 June 2006

• PuncAvg models can now deal with branch lengths that are undefined or zero

29 January 2006

• Fixed crashes at startup of calculations with single character and
  simulator.  Thanks to Karin Isler and Steve Kembel for reporting these
  bugs.

19 January 2006

• Updated license information and AppNote manuscript.

19 March 2005

• CoMET slimmed down.
• Feature added for custom punctuation definition.
• Simulation output filename is now user-specified.
• Updated User's Guide and AppNote

7 February 2005

• CoMET for single character is included.
• CoMET Simulator is included.
• Website now has updated User's Guide and short paper.

7 January 2005

• CoMET has been broken into proper Mesquite modules.
• Results are updated as tree and characters change.
• Results are written to the Mesquite log.
• User's Guide is updated.

16 December 2004

• Average models performance has been greatly improved! A 30-taxa tree now takes only seconds to compute and a few kilobytes of disk space thanks to reduced redundancy.

17 November 2004

• CoMET now prints shorter text output for results to better fit text in the output window.
• Some bad leftover code involving the Free models have been removed.
• Average models performance has been improved, but is still slow even for trees with 30+ taxa. The user is prompted for the option to skip these calculations.
• In order to accommodate trees larger than 255 nodes, new tricks will be needed for the Punctuate/Average mdoels. Current ideas include using taxa pairing matrices instead of just pairing sequences to reduce repeats. If the number of taxa is great enough, then these matrices may also need to be paged to disk.

Contacts

• chunghaulee@gmail.com
• Dr. Todd Oakley