Coalescent theory is a method often used by population geneticists in order to make inferences about evolutionary parameters. The coalescent is a stochastic model that approximates ancestral relationships among genes. An understanding of the coalescent pattern of a sample of sequences, along with some knowledge of the mutations that have occurred, provides information about the evolutionary forces that have acted on the population. Processes such as migration, recombination, variable population size, or natural selection are the forces that affect the genealogies and lead to genetic variability in a sample. Coalescent theory provides a statistical description of the variability in the sample, which in turn leads to inference about evolutionary parameters such as population size, population growth rates, and migration rates. Several methods have been developed that model the coalescent under different sets of evolutionary assumptions. We have examined and compared three computer packages that estimate parameters under the coalescent model: LAMARC, Genetree, and UPBLUE. These are not commercial computer programs, but have been developed by researchers for their own use and made available to others. Their performance in various areas has not been previously well established. We compared the programs in the general areas of model assumptions, availability, usability, and results. No single program is superior to the others in all areas, but each have strengths and weakness. Program selection must be based on the researcher's data, goals and preferences. This comparison should help population geneticists determine which program would be most applicable for their data and research.
College and Department
Physical and Mathematical Sciences; Statistics
BYU ScholarsArchive Citation
Shepherd, Kristen Piggott, "A Comparison of Coalescent Estimation Software" (2002). Theses and Dissertations. 21.
Coalescent, LAMARC, Genetree, UPBLUE, DNA data, population genetics, software