Dear Jose,

There are a number (quite a few more than MrBayes) of 16x16 stem RNA models implemented in HyPhy (available via StandardAnalyses>Basic Analyses>AnalyzeDiNucData.bf).

When you say you have only 8 states, I presume you mean that only 8 pairings (AU,UA,CG,GC,GU,UG and 2 more most likely) are actually observed in the alignment?

You could implement your analysis following the lines of, for example the file Examples/SimpleAnalyses/HKY85shared.bf, with a few tricks.

1). You need to create a doublet filter and explicitly exclude the 8 states you don't want to model. For example
Code:

DataSetFilter RNASomeStates = CreateFilter (myData,2,"","","AC,AG,UC");
 

would create a 13 state filter (16 states minus "AC,AG,UC"). This construct also assumes that your data are linearly arranged, i.e. the site 1 is paired with site 2,
site 3 with site 4 etc

2). When defining the rate matrix to model the evolution of your 8 states, it is important to understand how they are ordered (from 1st to last). For 16 states, the arrangement is lexicographic (AA,AC,AG,AU,....,UA,UC,UG,UU). For a reduced set, the ordering will be the same, except the excluded states won't be there. This mapping will help you define the rate matrix properly.

HTH,
Sergei

Dear Jose,

Yes, indeed, you could filter the alignment differently, without having to edit it at all. Which format do you currently use to identify paired nucleotides in an alignment? If you use the parenthetical notation, I have a converter file which will produce a filter for HyPhy to work on...

Cheers,
Sergei

Dear Jose,

If you have a list of pairing sites handy, you can easily stick it into HyPhy (with the caveat that HyPhy starts numbering from 0).

E.g.

DataSetFilter RNAData = CreateFilter (ds, 2, "0,5,1,4...

Alternatively, if you have runs of sites (e.g. 0-4 is paired with 15-11), you can write "0-4&15-11", to generate the list 0,15,1,14,2,13,3,12,4,11 etc

Also, HyPhy can read CHARSET blocks from NEXUS files if you have those...

Cheers,
Sergei

Just some more questions: how does HyPhy read PAUP's 'charset' command? What further steps do I need to put in datasetfilter so that such data is read properly? Does HyPhy automatically 0-index the sites?

Wow... those are really neat tricks... thks once more!