I am currently processing the dataset using MiSeq SOP and trying to create a dendrogram (for 8 samples) showing the bootstrap percentage values on nodes. I used Mothurâ€™s in-built Bray-Curtis dissimilarity to calculate a distance matrix, which was subsequently used in hierarchical clustering by UPGMA algorithm. However, when I view the dendrogram in MEGA, I am unable to see the bootstrap percentage values on nodes. Is there any way that I could obtain the bootstrap percentage values?
If you run tree.shared instead of dist.shared you should get a consensus tree out that has the pseudoboostrap values.
I always use tree.shared. I see branch length in the .tree file, but not the pseudobootstrap values that you mean. How can I get them ?
The consensus trees created by tree.shared set the branch label to the pseudo bootstrap value. When finding the consensus tree mothur looks at how many times each grouping occurs in each tree. Groupings are everything from a single node to the entire tree. For example combos FI and EGK would create a pair containing F and I and a pair E, G and K. If you saw the combo FI again in another tree you would then update update the count on the pair F and I to 2. Once the best tree is found, the counts for best grouping chosen at each node are divided by the number of trees used to find the consensus. So if FI was seen in 92 of the 100 trees, then the label would be set to 0.92.