A brief overview of the PTM algorithm. A brief overview of the PTM algorithm. In the first phase the taxa are sorted and grouped into small disjoint sets. A stepwise maximum parsimony tree is built from each of these sets. In the second phase these trees are repeatedly joined, refined, and divided. The division of trees is identical to the tree bisection portion of the TBR algorithm. Likewise, the joining of these trees is identical to the tree reconnection portion of TBR. For this joining to work, it is essential that no taxa is represented twice. To insure this, during a PTM search all leaves on all partial trees are uniquely labeled. In the final phase no division occurs. Thus, the trees continue to grow in size until a tree containing all of the taxa is produced.
Sundberg et al. BMC Bioinformatics 2012 13(Suppl 13):S8 doi:10.1186/1471-2105-13-S13-S8