Computational protocol: An experimental study of Quartets MaxCut and other supertree methods

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Protocol publication

[…] We used RAxML [], one of the most accurate ML phylogeny estimation methods. [...] We used MRP, using a very effective heuristic search technique called the Ratchet [] (see Appendix [Additional file ] for commands used). This returns a set of trees, each of which has the best (found) score; we then compute the greedy consensus (gMRP) tree for this set. The greedy consensus is a refinement of the majority consensus, and thus contains all the bipartitions present in more than half the input trees; it is a common consensus method, and in our experiments produces the most accurate supertrees when applied to results produced by the Ratchet. We also computed supertrees based upon three ways of encoding the source trees as sets of quartet trees and then applying QMC, as described above. Finally, we computed supertrees using five other methods: Q-Imp, RFS, MinFlip, SFIT, and PhySIC (See Appendix [Additional file ] for details on software and commands used).Because MinFlip, RFS, and PhySIC require that the source trees be rooted, we rooted each source tree at the midpoint of the longest leaf-to-leaf path (a standard method for rooting trees when there is no outgroup available) before passing the source trees to these three methods. […]

Pipeline specifications

Software tools RAxML, PhySIC
Application Phylogenetics