The MicrobesOnline tree comparison tool
run as follows:
compareTrees.missingBranch tree1.nwk tree2.nwk -simplify
which reports
| number of bipartitions | number of false negative bipartitions | the proportion of false negative bipartitions |
|---|
When run with -simplify the number of false negative bipartitions is equal to half of RF (Robinson and Foulds) distance
if internal nodes have labels, the command above might fail. The simplest solution is:
compareTrees.missingBranch <(nw_topology -bI tree1.nwk) <(nw_topology -bI tree2.nwk) -simplify
where nw_topology is a command in newick utilites.