Comparison of methods for estimating the nucleotide substitution matrix

Background: The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matrices, methods based on Markov triples, and maximum likelihood methods that infer the substitution probabilities that lead to the most likely model of evolution. However, the speed and accuracy of these methods has not been compared. Results: Different methods differ in performance by orders of magnitude (ranging from 1 ms to 10 s per matrix), but differences in accuracy of rate matrix reconstruction appear to be relatively small. Encouragingly, relatively simple and fast methods can provide results at least as accurate as far more complex and computationally intensive methods, especially when the sequences to be compared are relatively short. Conclusion: Based on the conditions tested, we re...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A. Huttley, Manuel E. Lladser, Rob Knight
• Keywords: BMCBI 2008, Molecular Evolution, Nucleotide Substitution Rate, Substitution Rate Matrix