jModelTest2

I had been having difficulties with jModelTest, and while searching for information about one of the problems I was having**, I discovered jModelTest2. I am quite surprised I hadn't come across it before, since it apparently has been around in some form or another for over a year, but I somehow failed to hear about it until now.

The first thing of note is that jModelTest2 can test all submodels of the GTR model. I am attempting to do this with my first trial to see how long it takes. Unlike jModelTest, jModelTest2 can use a hill-climbing algorithm to systematically find the best-fit models. Because the software I use (Phycas, MrBayes) doesn't accomodate all submodels, this may not be too relevant. However, BEAST or RevBayes can accomodate any submodel, so it may be useful in conjunction with those.

The second thing of note is high performance computing, supporting up to eight threads. Unfortunately, I don't really know much about this. My computer has a single-core processor, but it still seems to benefit from the threading. I may do a test run to see if the time it takes is dramatically reduced. Also not quite sure if "iddle" is a typo.

All-in-all, it seems like jModelTest2 is having no difficulties with the files that jModelTest threw errors for, so I take that as a good sign.

** In the old version of jModelTest, I was getting this error:

Notice "BIONJ-JC tree: null." This was the error I was trying to find more information on when I found out about jModelTest2.