Local Search for the Maximum Parsimony Problem

Four local search algorithms are investigated for the phylogenetic tree reconstruction problem under the Maximum Parsimony criterion. A new subtree swapping neighborhood is introduced and studied in combination with an effective array-based tree representation. Computational results are shown on a set of randomly generated benchmark instances as well as on 8 real problems (sequences of phytopathogen γ-proteobacteria) and compared with two references from the literature

On the Complexity of Parameterized Local Search for the Maximum Parsimony Problem

Maximum Parsimony is the problem of computing a most parsimonious phylogenetic tree for a taxa set X from character data for X. A common strategy to attack this notoriously hard problem is to perform a local search over the phylogenetic tree space. Here, one is given a phylogenetic tree T and wants to find a more parsimonious tree in the neighborhood of T. We study the complexity of this problem when the neighborhood contains all trees within distance k for several classic distance functions. For the nearest neighbor interchange (NNI), subtree prune and regraft (SPR), tree bisection and reconnection (TBR), and edge contraction and refinement (ECR) distances, we show that, under the exponential time hypothesis, there are no algorithms with running time |I|^o(k) where |I| is the total input size. Hence, brute-force algorithms with running time |X|^?(k) ? |I| are essentially optimal. In contrast to the above distances, we observe that for the sECR-distance, where the contracted edges are constrained to form a subtree, a better solution within distance k can be found in k^?(k) ? |I|^?(1) time

FPGAを用いた最節約法による進化系統樹構築アルゴリズムの高速化

筑波大学 (University of Tsukuba)201

Local Search for the Maximum Parsimony Problem

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