Greetings,

I have added (the long overdue) models of di-nucleotide evolution in RNA stems. The models can be accessed via StandardAnalyses->AnalyzeDiNucData.bf

The models implemented include:

• Modified Muse HKY85 (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login)
• Arbitraty 16 states reversible models, including RNA16A of Savill et al (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login)
• The model of Schoniger and von Haessler (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login) improved to allow an arbitrary nucleotide substitution biases

The input file is assumed to to consist of paired nucleotides which are arranged sequentially. You can try the models on the example RNA alignment in 'data'.

As a side benefit, result processing modules allow one to reconstruct ancestral RNA states.

Sergei