testnh-help-forum

Hi, I tried to prove the non-homogeneity with Testnh of a new model with parameters estimated by

Hello, I'd like to use bppml and testNH to replicate the substitution mapping procedure of

Dear Shea, Indeed, thanks a lot for reporting this! Best regards, Julien.

Should be fixed now :) J.

I must add that GAbrach is actually no more supported in HyPhy, because they say that their

Dear Paulina & Julien, yes indeed, the usual output of mapnh does not normalize the counts, so

Thanks a lot!! Now it worked!! Cheers! Paulina

Great ! Thanks a lot, Julien ! Le lundi 9 septembre 2013 15:05:42 UTC+2, Fidel Botero a écrit : Hello

OK Many thanks Sylvain On Thursday, August 29, 2013 9:54:07 PM UTC+2, Glémin Sylvain wrote: Hello, I

Hi Benoit, TestNH has not yet been updated to the newest version of Bio++. I mean, the packages are

Dear Julies, Thanks! Yes, I use MapNH. I try to use useObservedFreqs=yes as in the examples, but the

Hello! I just discover testnh and I would like to use it for Substitution mapping. Is it possible to

Hi Tristan, A good old issue... we really need to document that.1 is synonymous, 2 is nonsynonymous.

Dear Julien, Thanks for the quick response! Yes, I think that a flexible solution similar to the

Hi Tristan, in the usual codon models, indeed stop codons are not considered, perhaps because it is

Ok. See previous email for the compilation issue. J. On Fri, Sep 28, 2012 at 5:19 PM, Tristan

Hi Nguyen, For the branch lengths units, Laurent can answer better than me. In any case, this does

Hi, In this R script, I simply copy the tree.S into tree.dNdS, and then change the branch lengths to

Hi Nguyen, The "auto" clustering is for when Dn and Ds are two small. It is not that they

Hi Nguyen, Finally solved that bug, which occurred only when the homogenous model (1 partition) was

Hi, Indeed. One can also use Marginal(threshold=1), to ensure all categories are represented. In

Even in this case it is not so easy to make categories, because a codon is not only more of GCs or

Yes, but I found the .phy file in Mantellid. L On 11 juil, 13:52, Julien Yann Dutheil <jy.duth...@

Hi Laurent, That comes from the SubstitutionRegister class, but it is true that we should output this

Dear Nguyen, > 1. I get confusing in choosing what is the best partion from the following >

Hi Tristan, It is the maximum number of counts on a branch-site, to control for saturation. It is