I would like to create a phylogenetic tree from a structure-annotated alignment of RNA genes. Usually tree inference programs, even the software for rRNA analysis, uses standard single-base substitution models like HKY or GTR for all alignment positions.
So, which software can make use of the covariance information of the base pairs, e.g. in maximum likelihood approach, by using a base pair substitution model for paired columns. Be it either a parametrized model (7-state or more) or an empirical model (such as the subsone fromrdtitution matrix from pfold).
Any suggestions? Thanks, Peter