increase damping parameter to avoid oscillations in branch length optimization
@@ -1812,7 +1812,7 @@ class TreeAnc(object):
clade.up = node.up
- def optimize_tree_marginal(self, max_iter=10, infer_gtr=False, damping=0.5,
+ def optimize_tree_marginal(self, max_iter=10, infer_gtr=False, damping=0.75,
LHtol=0.1, site_specific_gtr=False):
self.infer_ancestral_sequences(marginal=True)
oldLH = self.sequence_LH()
