preserve profile map in gtr inference
@@ -217,8 +217,10 @@ class TreeAnc(object):
print('n_ij:', nij)
print('T_i:', Ti)
root_state = np.array([np.sum(self.tree.root.sequence==nuc) for nuc in alpha])
+
self._gtr = GTR.infer(nij, Ti, root_state, fixed_pi=fixed_pi, pc=5.0,
- alphabet=self.gtr.alphabet, logger=self.logger)
+ alphabet=self.gtr.alphabet, logger=self.logger,
+ prof_map = self.gtr.profile_map)
if normalized_rate:
self.logger("TreeAnc.infer_gtr: setting overall rate to 1.0...", 2)
self._gtr.mu=1.0
