Determining the evolutionary history of gene families

摘要: Motivation: Recent large-scale studies of individuals within a population have demonstrated that there is widespread variation in copy number many gene families. In addition, increasing evidence the can give rise to substantial phenotypic effects. some cases, these variations been shown be adaptive. These observations show full understanding evolution biological function requires an gain and loss. Accurate, robust evolutionary models loss events are, therefore, required. Results: We developed weighted parsimony maximum likelihood methods for inferring events. To test methods, we used Markov simulate data with known properties. examine three models: simple birth–death model, single rate model innovation parameters estimated from Drosophila genome data. find all simulations likelihood-based are very accurate reconstructing duplication on phylogenetic tree, similar accuracy ancestral state. Our implementations different provide inferences states For reconstruction, recommend because it has likelihood, but much faster. individual or events, noticeably more accurate, albeit at greater computational cost. Availability: www.bioinf.manchester.ac.uk/dupliphy Contact:simon.lovell@manchester.ac.uk; simon.whelan@manchester.ac.uk Supplementary information:Supplementary available Bioinformatics online.