def test_gtr(self):
f = [0.23, 0.31, 0.21]
s = sum(f)
f.append(1.0-s)
gtr = RevDiscreteModel(r_upper=[[1.0, 3.0, 1.2], [2.0, 4.1],[0.8]],
equil_freq=f)
m = gtr.get_probs(0.01)
assert_mat_eq(self, m, [[0.99204347826086958, 0.0019969565217391304, 0.0040317391304347822, 0.001926086956521739],
[0.0014816129032258064, 0.98928709677419346, 0.0026880645161290323, 0.0065419354838709672],
[0.0044157142857142858, 0.0039680952380952384, 0.9903238095238095, 0.0012942857142857144],
[0.0017719999999999999, 0.0081119999999999994, 0.0010872, 0.98902800000000002]])
