Triplet MaxCut: a new toolkit for rooted supertree

Abstract

Summary The rapid increase of molecular, as well as other types, of available classification data has created the need to combine this data into a unified hypothesis. Supertree methods are essential when amalgamating phylogenetic information from various, possibly conflicting, sources into a single tree. The goal of a supertree algorithm is to satisfy maximally each such source of information in the output tree. Triplets, rooted trees over three leaves, are the minimal piece of such information when dealing with rooted trees. Due to its fundamental role in phylogenetics, extensive effort has been dedicated to several aspects regarding triplets’ research. We have devised a new tool, Triplet MaxCut (TMC), performing various operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility and efficiency of the algorithm is demonstrated by both simulation study and four real data supertree inputs.