hello,

I'm working with some data where the ancestor is known independently (alignments between ancestral transposons and modern sequence). I would like to determine rate parameters in as much detail as possible, ideally all 12 nondiagonal rates. I think this means I want a non-reversible model.

Is this possible to do in HYPHY? If so, is there some way I need to indicate which sequence is the ancestor?

thanks!

Hi Weli, there are two batch files you should look at.

NRM.mdl and NRM+Freqs.mdl.

Both of these implement a non-reversible model, yet differ in how they deal with stationary frequencies.

You may want to look at this thread which discusses these options in detail.

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cheers ./w

and use

ACCEPT_ROOTED_TREES = 1;

in your batch file.

./w

Thanks, that helps a lot. One more question about specifying an ancestor.

I did the following

ACCEPT_ROOTED_TREES = 1;
Tree      Tr =  (anc,der);

which gives me this output:

Tree Tr=(anc:0.125158,der:0.195086);

It looks like its put the root somewhere between anc and der, and is still treating them as tips. I want to force it to make anc the ancestor. Is there any way to do that?

thanks again.

hi, a two taxon tree is by default unrooted. However, in your case you can force an ancestor by constraining the branch length of the ancestor to be 0.

ie.

Tr.anc.t := 0;

./w