A Simulation Study Comparing Supertree and Combined Analysis Methods Using SMIDGen

Background: Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the “supertree”) on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a “supermatrix” or “total evidence” approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix. Results: In this paper, we describe an extensive simulation study we performed comparing two supertree methods, MRP and weighted MRP, to combined analysis methods on large model trees. A key contribution of this study is our novel simulation methodology (Super-Method Input Data Generator, or SMIDGen) that ...

• Type: Conference
• Year: 2009
• Where: WABI
• Authors: M. Shel Swenson, François Barbançon, C. Randal Linder, Tandy Warnow
• Keywords: Algorithms, Better Supertree Methods, Combined Analysis, Supertree Methods, WABI 2009