COMET : COalescent with Multiple mergers Employing Thermodynamic integration
COMET is a program for MCMC-based sampling of multiple mergers genealogies based on multiple mergers coalescent models. [1-4]
It can be used with different BETA settings for running chains at various heats so that marginal probabilities of
models can be computed using thermodynamic integration [5,6].
COMET was conceived by John B. Horne, PhD, Edward A. Salinas, MS and Rita Castilho, PhD. Edward A. Salinas is the programmer.
COMET has been accepted for poster presentation at the 2015 Great Lakes Bioinformatics Conference (GLBIO 2015 ; May 18-20, 2015) at poster session B, poster #38. The conference was held at Purdue University in W. Lafayette, IN.
A copy of the submitted/accepted abstract is available here.
A PDF version of the presented poster is available here.
The code/program is accessible via a bitbucket git repository here.
A slideshow providing an overview, information, and status as of late Spring 2015 can be found here.
A slideshow providing notes on recent developments in Proposal Schems for Multiple Mergers genealogies as of Nov 9th, 2015 can be found here.
References :
1. Sargsyan, Ori and Wakeley, John, A coalescent process with simultaneous multiple mergers for approximating the gene genealogies of many marine organisms, Theoretical Population Biology 74 (2008) 104-114
2. Coalescent Theory: An Introduction, John Wakeley, Greenwood Village, CO: Roberts and Company,2008
3. Yang, Ziheng (2014) Molecular Evolution : A Statistical Approach , Oxford University Press
4. Aurelien Tellier, Christophe Lemaire, Coalescence 2.0: a multiple branching of recent theoretical developments and their applications, Molecular Ecology Vol. 23, No. 11, pp 2637-2652, June 2014
5. Lartillot, N. and H. Philippe, Computing Bayes Factors Using Thermodynamic Integration, Syst. Biol. 55(2):195-207,2006
6. Beerli, Peter and Palczewski, Michal, Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations, Genetics 185: 313-326 (May 2010)
Contact information :
Edward A. Salinas : eddie At eddie salinas.com
