The maximum agreement forest problem: Approximation algorithms and computational experiments

Rodrigues, Estela Maris; Sagot, Marie‐France; Wakabayashi, Yoshiko

doi:10.1016/j.tcs.2006.12.011

Cited by 34 publications

(44 citation statements)

References 4 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The approximation ratio was improved to 3 by Bordewich et al (2008), but at the expense of an increased running time of O(n 5 ). A second 3-approximation algorithm presented in Rodrigues et al (2007) achieves a running time of O(n 2 ). Recently, Whidden and Zeh (2009), Whidden et al (2011) presented a linear-time approximation algorithm of ratio 3, which is the best known approximation algorithm for the Maximum Agreement Forest problem on two rooted binary phylogenetic trees.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Improved approximation algorithm for maximum agreement forest of two rooted binary phylogenetic trees

Shi

Jie

et al. 2015

J Comb Optim

View full text Add to dashboard Cite

Given two rooted binary phylogenetic trees with identical leaf label-set, the maximum agreement forest (MAF) problem asks for a largest common subforest of the two trees. This problem has been studied extensively in the literature, and has been known to be NP-complete and MAX SNP-hard. The previously best ratio of approximation algorithms for this problem is 3. In this paper, we make full use of the special relations among leaves in phylogenetic trees and present an approximation algorithm with ratio 2.5 for the MAF problem on two rooted binary phylogenetic trees.

show abstract

Section: Introductionmentioning

confidence: 99%

“…For the MAF problem on two rooted general phylogenetic trees, Rodrigues et al (2007) developed an approximation algorithm of ratio d + 1, where d is the maximum number of children a node in the input trees may have. Later Lersel et al (2014) presented a constant ratio 4-approximation algorithm.…”

Section: Introductionmentioning

confidence: 99%

Improved approximation algorithm for maximum agreement forest of two rooted binary phylogenetic trees

Shi

Jie

et al. 2015

J Comb Optim

View full text Add to dashboard Cite

show abstract

“…We aim at partitioning the set of species S into a minimum number of subsets S 1 ,..., S k such that for each subset S i , the two subtrees T S ( S i ) and T G ( S i ) agree, and all T S ( S i ) as well as all T G ( S i ) are disjoint. We call this partition a maximal statistical agreement forest (MSAF), in reference to the maximal agreement forest [8,9], which is the particular case where the agreement function gives a positive answer only if the two compared (sub-)trees are homomorphic (have the same topology).…”

Section: Resultsmentioning

confidence: 99%

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

et al. 2010

View full text Add to dashboard Cite

BackgroundTo understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.ResultsWe present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.ConclusionsThe ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier

show abstract

“…Unfortunately, it is NP-hard to compute the rSPR distance of two given phylogenetic trees [5,11]. This has motivated researchers to design approximation algorithms for the problem [3,4,11,16]. Hein et al [11] were the first to come up with an approximation algorithm.…”

Section: Introductionmentioning

confidence: 99%

A New 2-Approximation Algorithm for rSPR Distance

Chen

Harada

Wang

2017

Bioinformatics Research and Applications

View full text Add to dashboard Cite

Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to measure the dissimilarity of the two trees. The rooted subtree prune and regraft (rSPR) distance of the two trees has been used for this purpose. The problem of computing the rSPR distance of two given trees has many applications but is NP-hard. The previously best approximation algorithm for rSPR distance achieves a ratio of 2 in polynomial time and its analysis is based on the duality theory of linear programming. In this paper, we present a cubic-time approximation algorithm for rSPR distance that achieves a ratio of 2. Our algorithm is based on the notion of key and several structural lemmas; its analysis is purely combinatorial and explicitly uses a search tree for computing rSPR distance exactly.

show abstract

The maximum agreement forest problem: Approximation algorithms and computational experiments

Cited by 34 publications

References 4 publications

Improved approximation algorithm for maximum agreement forest of two rooted binary phylogenetic trees

Improved approximation algorithm for maximum agreement forest of two rooted binary phylogenetic trees

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

A New 2-Approximation Algorithm for rSPR Distance

Contact Info

Product

Resources

About