The study of phylogenetic networks is of great interest to computational evolutionary biology and numerous different types of such structures are known. This article addresses the following question concerning rooted versions of phylogenetic networks. What is the maximum value of pset membership, variant[0,1] such that for every input set T of rooted triplets, there exists some network View the MathML source such that at least p|T| of the triplets are consistent with View the MathML source? We call an algorithm that computes such a network (where p is maximum) worst-case optimal. Here we prove that the set containing all triplets (the full triplet set) in some sense defines p. Moreover, given a network View the MathML source that obtains a fraction p′ for the full triplet set (for any p′), we show how to efficiently modify View the MathML source to obtain a fraction greater-or-equal, slantedp′ for any given triplet set T. We demonstrate the power of this insight by presenting a worst-case optimal result for level-1 phylogenetic networks improving considerably upon the 5/12 fraction obtained recently by Jansson, Nguyen and Sung. For level-2 phylogenetic networks we show that pgreater-or-equal, slanted0.61. We emphasize that, because we are taking |T| as a (trivial) upper bound on the size of an optimal solution for each specific input T, the results in this article do not exclude the existence of approximation algorithms that achieve approximation ratio better than p. Finally, we note that all the results in this article also apply to weighted triplet sets.
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Journal of Discrete Algorithms
Networks and Optimization

Byrka, J., Huber, K. T., Kelk, S., & Gawrychowski, P. (2009). Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. Journal of Discrete Algorithms, (0710.3258), 1–17.