Hi Sergei,
I am running the YangNielsenBranSite2005 analysis and I am continually getting worse scores for my Alternate model than for I am for Null for Test 2.  I have tried increasing the optimisation precision and the number of iterations per variable to

OPTIMIZATION_PRECISION = 0.00001;
MAXIMUM_ITERATIONS_PER_VARIABLE=1000;

but I am now not getting convergence for my alternate hypothesis.

I have run the PAML branch site test on the same data and it is reporting higher likelihood scores than HYPHY for both the Alternate hypothesis and the Null for Test 2. For other tests I usually find the programs agree to within a few decimal places as you have stated in my previous post so I am very interested in figuring out why the results are off this time.

I have two questions.

1) If I am getting a worse likelihood score for the Alternate hypothesis should I take that to mean I shouldn't reject the Null hypothesis. Or should I take that to mean the function is not converging and I need to increase the number of iterations and the precision further?

2) What precision level should I be using to get the same results as PAML and how many iterations should be necessary to get convergence for the likelihood function? Also is there anyway to speed up the convergence?

As always thank you for the help.

Sincerely,
Andrew