LG Substitution Model in BEAST2?

[davi...@yahoo.com]

Hi All:
I have been using the LG amino acid substitution model in BEAST 1.8.3.  I decided to try BEAST2, but the BEAUTi options with that package do not seem to include the LG model.  Was that model deliberately excluded from the later release for some reason that I should know about (poor performance somehow?), or was this an oversight?  Is there any plan to reinsert that option in a later version?
Thanks,
Dave Kerk

[Remco Bouckaert]

Hi Dave,

The LG model is available by installing the beast-classic package (v1.2.1). 

After installing (and restarting BEAUti) it should show up in the substitution model choices under the site model panel in BEAUti.

Cheers,

Remco

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[David Kerk]

Hi Remco:

Thanks for your reply.  I need to clarify to make sure I understand properly.

Is this a procedure to tweak the BEAUTi GUI to show the LG model, which you can then use to prepare xml files for BEAST2?

Or are you saying that one needs to stay in the BEAST programs 1.X.X (not BEAST2) to run the LG model?

Also: after I had posted my message, I got the idea that perhaps the BEAST2 program will run the LG model but the new BEAUTi GUI just does not have that drop-down option?  So could one just manually find the statement in the xml file where the AA substitution model is specified, and replace say WAG with LG?  Would that work also?

Thanks again for your kindness in replying.

Best,

Dave

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[Remco Bouckaert]

Hi Dave,

BEAST 2 has packages that can be installed separately, and have their own version numbers. To use the LG model, you should install the latest version of a package called “beast-classic”, which is version v1.2.1.

The easiest way to install packages is through BEAUti, using the File/Manage packages menu (more details here: http://beast2.org/managing-packages/).

Once the package is installed, the LG model is available in BEAUti (after restarting BEAUti) and you can run BEAST on XML files where the LG model is selected.

Hope this clarifies things,

Remco