Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNA
Fig 6
Using the association index to determine informativeness of individual sites.
Schematic summary of the steps used to investigate site informativeness. Individual alignment positions are sequentially analysed for their concordance to a global phylogeny. Base identity is used to assign groups which are then use for calculation of an association value through group segregation in a neighbour-joining tree of the alignment where non-bootstrap supported branches are collapsed. The AI index is its ratio to the mean association value of 10 sequence label order randomised controls (representing the null expectation of no association). Finally, the Shannon entropy score, representing site heterogeneity is recorded.