Figure 1

Covarying mutations in an RNA alignment. (a) A multiple RNA alignment and its phylogenetic tree. Three pairs of columns, which are marked with different colors, are analyzed in the following three sub-figures. (b) Possible covarying mutations in the red columns. In this case, only one pair-wise mutation is required at the root node. (c) Possible covarying mutations in the green columns. At least two pair-wise mutations occur at the internal nodes in this case; (d) Possible covarying mutations in the blue columns. There are non-pairing bases, ‘AG’ and ‘A-’. The label inference of the internal nodes does not depend on them. So in this case, the number of mutations is one.