SuperTriplets is a triplet-based supertree approach to phylogenomics. It infers supertrees with branch support values.

Phylogenetic tree-building methods use molecular data to describe the evolutionary relationships among genes and taxa, and to infer biodiversity evolutionary patterns. A recurrent problem is to reconcile the various phylogenies built from different genomic sequences into a single one. SuperTriplets relies on a triplet-based representation of source trees to accomplish this task. Using this representation, the parsimony analysis is related to the median tree notion. SuperTriplets is specially designed to optimize this alternative formulation of the supertree problem.

SuperTriplets can easily handle large datasets. When the correct resolution of every triplet appears more often than the incorrect ones in source trees, SuperTriplets warrants to reconstruct the correct phylogeny. Both simulations and case studies on mammalian phylogenomics confirm the advantages of this approach. In both cases, SuperTriplets tends to propose less resolved but more reliable supertrees than those inferred using Matrix Representation with Parsimony (MRP).

For further details about the underlying algorithm see the original publication:
SuperTriplets: a triplet-based supertree approach to phylogenomics. Ranwez V, Criscuolo A, Douzery EJ. Bioinformatics. 2010 Jun 15;26(12):i115-23. doi: 10.1093/bioinformatics/btq196. PMID: 20529895; PMCID: PMC2881381.
PLoS One 2011, 6(9): e22594