2012
DOI: 10.1109/tcbb.2011.157
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A Metric for Phylogenetic Trees Based on Matching

Abstract: Comparing two or more phylogenetic trees is a fundamental task in computational biology. The simplest outcome of such a comparison is a pairwise measure of similarity, dissimilarity, or distance. A large number of such measures have been proposed, but so far all suffer from problems varying from computational cost to lack of robustness; many can be shown to behave unexpectedly under certain plausible inputs. For instance, the widely used Robinson-Foulds distance is poorly distributed and thus affords little di… Show more

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Cited by 68 publications
(29 citation statements)
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“…Individual cells are then chosen uniformly from the nodes in this topology until 250 cells are sampled. Because the true and inferred trees may have different node sets, we evaluate accuracy by a variant of the weighted matching metric of (Lin et al , 2012), seeking a maximum matching of phylogenetic bipartitions between true and inferred trees with each bipartition weighted according to the fraction of nodes it shares with its paired bipartition in the other tree. The total agreement in nodes across all bipartitions provides a fractional accuracy of the inference.…”
Section: Methodsmentioning
confidence: 99%
“…Individual cells are then chosen uniformly from the nodes in this topology until 250 cells are sampled. Because the true and inferred trees may have different node sets, we evaluate accuracy by a variant of the weighted matching metric of (Lin et al , 2012), seeking a maximum matching of phylogenetic bipartitions between true and inferred trees with each bipartition weighted according to the fraction of nodes it shares with its paired bipartition in the other tree. The total agreement in nodes across all bipartitions provides a fractional accuracy of the inference.…”
Section: Methodsmentioning
confidence: 99%
“…Since the reference trees used in our experiments are typically very topologically different from the true gene tree (8% RF distance for the moderate ILS condition, 33% for the high ILS condition, 54% to 68% for the ILS+HGT conditions, see Table 1), optimizing the RF distance to the reference tree is quite different from optimizing the RF distance to the true gene tree. Finally, we also evaluated the methods using the matching distance [32] and the quartet distance [33].…”
Section: Evaluation Criteriamentioning
confidence: 99%
“…We computed a maximum matching of edges between the real subtree and the inferred tree, with each pair of edges weighted by the maximum number of nodes in agreement between the corresponding parts of the bipartitions that the two edges define [46], [51]. We used the Hungarian algorithm [52] for computing the maximum matching (applying the function“Hungarian” by Alexander Melin from the Matlab Central File Exchange).…”
Section: Resultsmentioning
confidence: 99%