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Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data
Background: Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous ...
Phylogenomic analysis of natural selection pressure in Streptococcus genomes
Background: In comparative analyses of bacterial pathogens, it has been common practice to discriminate between two types of genes: (i) those shared by pathogens and their non-pathogenic relatives (core genes), and (ii) ...