how to set HIVw+R6 substitution model in bppsuite?

[lwang....@gmail.com]

Dear Bio++ team,

I got best substitution model (HIVw+R6) from ModelFinder for our dataset. I was wondering how to set HIVw+R6 (FreeRate model with 6 categories) in bppsuite?

Best regards,

Liang

[Laurent Guéguen]

Dear Liang,

if it is not already there, it has to be defined. Could you give me the article reference to this model?

Cheers,

Laurent

[lwang....@gmail.com]

Dear Laurent,

The paper described the HIVw (within individual, HIV within, HIV-Wm) substitution model was attached.  Thank you for your quick response. I am looking forward to your guidance.

Best regards,

Liang

[Julien Y. Dutheil]

Hi,

They seem to provide the subsitution matrices http://www.hyphy.org/pubs/HIV-model/. With a bit of luck (and maybe also reformating), they could be directly read in bpp suite as a user defined model?

Julien.

[lwang....@gmail.com]

Dear Laurent,

Thank you for you quick response. I have found this folder before. however, since I am new in bppsuite, I have no idea which file could be used to reformat, and also how to reformat. Is there any possible to guide me which file should I use and how to re-format the file to generate the HIVw substitution model?

Best regards,

Liang

[Julien Y. Dutheil]

Dear Liang,

See http://biopp.univ-montp2.fr/manual/html/bppsuite/2.4.0/bppsuite.html#Protein, the "Empirical" option. The input files should be formatted following the PAML format (see .dat files in the PAML package).

Hope this helps,

Julien.