From a0c45b71b8c85ffee663fb249668b21518aa644f Mon Sep 17 00:00:00 2001
From: jordandouglas <jordandouglas@windowslive.com>
Date: Fri, 28 Apr 2023 11:29:37 +1200
Subject: [PATCH] allow for cognate singletons

---
 .../StochasticDolloTreeLikelihoodFast.java         | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/src/indeldollo/StochasticDolloTreeLikelihoodFast.java b/src/indeldollo/StochasticDolloTreeLikelihoodFast.java
index 08fa04f..80b8722 100644
--- a/src/indeldollo/StochasticDolloTreeLikelihoodFast.java
+++ b/src/indeldollo/StochasticDolloTreeLikelihoodFast.java
@@ -184,12 +184,20 @@ public double calculateLogP() {
 		// Mean birth rate (weighted by branch lengths)
         double totalWeightedRate = 0.0;
         double totalTreeLength = 0.0;
-        for (Node node : root.getAllChildNodesAndSelf()) {
-        	double rate = branchRateModel.getRateForBranch(node);
-        	double length = node == root ? (birthTime - node.getHeight()) : node.getLength();
+        if (root.isLeaf()) {
+        	double rate = branchRateModel.getRateForBranch(root);
+        	double length = birthTime - root.getHeight();
             totalWeightedRate += rate * length;
             totalTreeLength += length;
+        }else {
+        	for (Node node : root.getAllChildNodesAndSelf()) {
+            	double rate = branchRateModel.getRateForBranch(node);
+            	double length = node == root ? (birthTime - node.getHeight()) : node.getLength();
+                totalWeightedRate += rate * length;
+                totalTreeLength += length;
+            }
         }
+        
         double meanBranchRate = totalWeightedRate/totalTreeLength;
         double meanBirthRate = lambda * mutationRate * meanBranchRate;