only add sequence LH to total if reconstruction has been performed
@@ -476,7 +476,7 @@ class ClockTree(TreeAnc):
LH -= node.branch_length_interpolator(node.branch_length)
# add the root sequence LH and return
- if self.aln:
+ if self.aln and self.sequence_reconstruction:
LH += self.gtr.sequence_logLH(self.tree.root.cseq, pattern_multiplicity=self.data.multiplicity)
return LH
