Faster exact computation of rSPR distance

Chen, Zhizhong; Fan, Ying; Wang, Lusheng

doi:10.1007/s10878-013-9695-8

Cited by 13 publications

(10 citation statements)

References 17 publications

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“…Although the time complexity of the best algorithm [38] for the Maximum Agreement Forest problem on two rooted binary phylogenetic trees, which is O(2.344 k n), is better than that of our algorithm Alg-hMaf, the methods of the algorithm in [38] seem difficult to extend to solving the hMaf problem.…”

Section: Resultsmentioning

confidence: 80%

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A parameterized algorithm for the Maximum Agreement Forest problem on multiple rooted multifurcating trees

Shi

Chen

et al. 2018

Journal of Computer and System Sciences

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Section: Resultsmentioning

confidence: 80%

“…Whidden et al [37] improved this bound and developed an algorithm of running time O(2.42 k k + n 3 ). Chen et al [38] presented an algorithm of running time O(2.344 k n), which is the best known result of the Maximum Agreement Forest problem on two rooted binary phylogenetic trees.…”

Section: Introductionmentioning

confidence: 99%

A parameterized algorithm for the Maximum Agreement Forest problem on multiple rooted multifurcating trees

Shi

Chen

et al. 2018

Journal of Computer and System Sciences

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“…A 2.5-approximation algorithm for the MAF problem on two rooted binary phylogenetic trees is presented in Shi et al (2016). In Chen et al (2015) an FPT algorithm for rooted SPR, with complexity O(2.344 k · n) is presented, which is an improvement compared to O(2.42 k · n) (Whidden et al 2010). Rooted SPR is investigated also for non binary trees (Whidden et al 2016), and MAF for multiple trees (Chen et al 2016).…”

Section: A Review Of Previous Resultsmentioning

confidence: 99%

Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Hasic

Tannier

2019

J Comb Optim

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Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the gene level like duplication or transfer. These differences are handled by phylogenetic reconciliation, which formally is a mapping between gene tree nodes and species tree nodes and branches. We investigate models of reconciliation with a gene transfer that replaces existing gene, which is a biological important event but never included in reconciliation models. Also the problem is close to a dated version of the classical subtree prune and regraft (SPR) distance problem, where a pruned subtree has to be regrafted only on a branch closer to the root. We prove that the reconciliation problem including transfer and replacement is NP-hard, and that if speciations and transfers with replacement are the only allowed evolutionary events, then it is fixed-parameter tractable (FPT) with respect to the reconciliation's weight. We prove that the results extend to the dated SPR problem.Keywords phylogenetic reconciliation · dated subtree prune and regraft SPR · gene transfer · transfer with replacement (replacing transfer) · NP hard/complete · fixed parameter tractable FPT

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“…For small instances, that is, when the compared trees are rather similar, exact exponential algorithms work reasonably fast. We have tested the SPRDist application (Wu, 2009), which was able to compute all our test cases (each test case consists of 1000 comparisons between randomly generated pair of trees) of size up to 20 leaves, and UltraNet (Chen et al, 2015) able to compute test cases up to 40 leaves. For test cases with 50 leaves UltraNet (which worked much faster than SPRDist) was able to compute only 25 distances in about 5 days on a desktop computer, so we decided to interrupt further computation of the exact rSPR distance.…”

Section: Heuristics For Rooted Subtree Prune and Regraft Distance: Anmentioning

confidence: 99%

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions

Bogdanowicz

Giaro

2017

Journal of Computational Biology

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Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.

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Faster exact computation of rSPR distance

Cited by 13 publications

References 17 publications

A parameterized algorithm for the Maximum Agreement Forest problem on multiple rooted multifurcating trees

A parameterized algorithm for the Maximum Agreement Forest problem on multiple rooted multifurcating trees

Gene tree reconciliation including transfers with replacement is NP-hard and FPT

Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions

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