Phylogenetic Tree Inference Of Rna Sequences With Covariance Substitution Models

Question

[Peter]

Hi Biostar,

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

Answer 1

[Casey Bergman]

Try PHASE, whose features include:

• Bayesian estimation of phylogenies and substitution model parameters
• flexible choice of prior distributions and hierarchical models
• standard ML search algorithms for inferring the optimal tree
• optional user-specified constraints on the space of tree topologies
• computation of pairwise ML distances
• 6, 7 and 16 state RNA models
• standard 4 state DNA models
• empirical amino-acid models and one codon model
• invariant and discrete gamma model for substitution rate heterogeneity between sites
• mixing of molecular data types in a single analysis

[Peter]

thanks Casey, I will try this one. cheers, Peter