- Boot Split Distance (BSD)
The Boot Split Distance (BSD) method is an extension of the previously developed Split Distance (SD) method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on their bootstrap support. In the distance calculation by the BSD method, the tree splits are given weights proportional to their bootstrap support.
How to run: the value of the parameter '-m' must be 'bsd' to run the BSD method. Optionally a bootstrap threshold may be introduced using the parameter -th.
$ perl topd_v4.6.pl -f file -c [single/reference/multiple] -m bsd -th [no/50-100/500-1000]
To interpret the output see article: PMID:22399455