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Robinson-Foulds Supertrees

Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
2010 Algorithms for Molecular Biology  
Supertree methods based on the well established Robinson-Foulds (RF) distance have the potential to build supertrees that retain much information from the input trees.  ...  Specifically, the RF supertree problem seeks a binary supertree that minimizes the sum of the RF distances from the supertree to the input trees.  ...  Acknowledgements We thank Harris Lin for providing software for the triplet supertree analyses. This work was supported in part by NESCent and by NSF grants DEB-0334832 and DEB-0829674.  ... 
doi:10.1186/1748-7188-5-18 pmid:20181274 pmcid:PMC2846952 fatcat:6xilqhzbovdg3g5buktx3wzkze

Fast Local Search for Unrooted Robinson-Foulds Supertrees

R. Chaudhary, J. G. Burleigh, D. Fernandez-Baca
2012 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
A Robinson-Foulds (RF) supertree for a collection of input trees is a tree containing all the species in the input trees that is at minimum total RF distance to the input trees.  ...  Thus, an RF supertree is consistent with the maximum number of splits in the input trees. Constructing RF supertrees for rooted and unrooted data is NP-hard.  ...  In contrast to MRP, the Robinson-Foulds (RF) supertree method seeks a supertree that minimizes the total RF distance to the input phylogenies [13] .  ... 
doi:10.1109/tcbb.2012.47 pmid:22431553 fatcat:n4rryzpurfbsvdkxoyobjft53i

Fast Local Search for Unrooted Robinson-Foulds Supertrees [chapter]

Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
2011 Lecture Notes in Computer Science  
Fast Local Search for Unrooted Robinson-Foulds Supertrees 185 edit operation.  ...  A Robinson-Foulds (RF) supertree for a collection of input trees is a comprehensive species phylogeny that is at minimum total RF distance to the input trees.  ...  In contrast to MRP, the Robinson-Foulds (RF) supertree method seeks a supertree that minimizes the total RF distance to the input phylogenies [2] .  ... 
doi:10.1007/978-3-642-21260-4_20 fatcat:65mgtbuhcvervm3y6rcrdrikj4

Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees

Xilin Yu, Thien Le, Sarah Christensen, Erin K. Molloy, Tandy Warnow, Nadia Pisanti, Carl Kingsford
2020 Workshop on Algorithms in Bioinformatics  
Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation  ...  that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard.  ...  Thus, the Robinson-Foulds Supertree problem takes as input the profile A and seeks a Robinson-Foulds (RF) supertree for A, which we denote by RFS(A).  ... 
doi:10.4230/lipics.wabi.2020.15 dblp:conf/wabi/YuLCMW20 fatcat:mk4mbekbfzechnzddhcstrywii

Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation

Xilin Yu, Thien Le, Sarah A. Christensen, Erin K. Molloy, Tandy Warnow
2021 Algorithms for Molecular Biology  
Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation  ...  that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard.  ...  Thus, the Robinson-Foulds Supertree problem takes as input the profile A and seeks a Robinson-Foulds (RF) supertree for A , which we denote by RFS(A).  ... 
doi:10.1186/s13015-021-00189-2 pmid:34183037 fatcat:y4gpmtrkbncq3em3bypsthmuye

FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization

Pranjal Vachaspati, Tandy Warnow
2016 Bioinformatics  
Results: We present FastRFS, a new method based on a dynamic programming method we have developed to find an exact solution to the Robinson-Foulds Supertree problem within a constrained search space.  ...  Supertree estimation is itself NPhard, and no current supertree method has sufficient accuracy and scalability to provide good accuracy on the large datasets that supertree methods were designed for, containing  ...  The dynamic programming algorithm to solve constrained Robinson-Foulds supertrees While the Robinson-Foulds Supertree problem is stated in terms of minimizing the total Robinson-Foulds distance to the  ... 
doi:10.1093/bioinformatics/btw600 pmid:27663499 pmcid:PMC5870905 fatcat:u63ajbs2uzcmhmfg4t2t2gbvzu

Building alternative consensus trees and supertrees using k-means and Robinson and Foulds (RF) distance [article]

Nadia Tahiri, Bernard Fichet, Vladimir Makarenkov
2022 arXiv   pre-print
We show how an adapted version of the popular k-means clustering algorithm, based on some interesting properties of the Robinson and Foulds distance, can be used to partition a given set of trees into  ...  The output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree.  ...  Because the Robinson and Foulds distance is a symmetric difference distance , its square root (RF 1/2 ) is Euclidean.  ... 
arXiv:2103.13343v4 fatcat:sq6c2gj6tbhnhjq5n65cbpygsq

Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance [article]

Nadia Tahiri, Bernard Fichet, Vladimir Makarenkov
2021 bioRxiv   pre-print
We show how a specific version of the popular k-means clustering algorithm, based on some interesting properties of the Robinson and Foulds topological distance, can be used to partition a given set of  ...  The output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree.  ...  distance (Robinson and Foulds 1981) .  ... 
doi:10.1101/2021.03.24.436812 fatcat:6e4pbkhtdfcgjmsij45ecxtpbu

An Experimental Study of Quartets MaxCut and Other Supertree Methods [chapter]

M. Shel Swenson, Rahul Suri, C. Randal Linder, Tandy Warnow
2010 Lecture Notes in Computer Science  
In this paper, we evaluate the performance of several supertree methods based upon the Quartets MaxCut method of Snir and Rao.  ...  We show that two of these methods usually outperform MRP and all other supertree methods we studied under many realistic model conditions.  ...  Comparing QMC(Exp+TSQ) to Other Supertree Methods We compared QMC(Exp+TSQ) to six other supertree methods: gMRP, Q-Imp, SFIT, MinFlip, PhySIC, and Robinson-Foulds Supertrees (RFS).  ... 
doi:10.1007/978-3-642-15294-8_24 fatcat:atvv6rny2va25fgmr3wwigcywe

An experimental study of Quartets MaxCut and other supertree methods

M Shel Swenson, Rahul Suri, C Randal Linder, Tandy Warnow
2011 Algorithms for Molecular Biology  
In this paper, we evaluate the performance of several supertree methods based upon the Quartets MaxCut method of Snir and Rao.  ...  We show that two of these methods usually outperform MRP and all other supertree methods we studied under many realistic model conditions.  ...  Comparing QMC(Exp+TSQ) to Other Supertree Methods We compared QMC(Exp+TSQ) to six other supertree methods: gMRP, Q-Imp, SFIT, MinFlip, PhySIC, and Robinson-Foulds Supertrees (RFS).  ... 
doi:10.1186/1748-7188-6-7 pmid:21504600 pmcid:PMC3101644 fatcat:abinzfyxmveplhcfgwujwjxxae

Supertree Construction: Opportunities and Challenges [article]

Tandy Warnow
2018 arXiv   pre-print
In this paper, we describe the current state of the art in supertree construction and the use of supertree methods in divide-and-conquer strategies.  ...  Because most supertree methods are heuristics for NP-hard optimization problems, the use of supertree estimation on large datasets is challenging, both in terms of scalability and accuracy.  ...  The first divide-and-conquer methods (DCM-NJ, DACTAL, etc.) were developed with CIPRES support, as were the supertree methods SuperFine and the Strict Consensus Merger that enabled those divide-and-conquer  ... 
arXiv:1805.03530v1 fatcat:sl6btuirxzcqpk62t66buxavge

Research Article Impact of ancient oxygen levels on mitochondrial genome evolution inferred by supertrees, supermatrices, and relaxed molecular clocks

L.R. Lopes, R.C. Ferreira, F. Antoneli, P.B. Paiva, M.R.S. Briones
2021 Genetics and Molecular Research  
The branching patterns did not differ substantially in supertrees and supermatrix phylogenies.  ...  We produced phylogenomic supertrees and a supermatrix tree of 46 mitochondrial genomes, showing that the loss of complex I predates WGD and occurred independently in the S. cerevisiae group and the fission  ...  RF Supertree was inferred using the Robinson-Foulds algorithm as implemented in the RF program (Bansal et al. 2010).  ... 
doi:10.4238/gmr18485 fatcat:yy6anlkv5zb5zj5ixsbtedjzg4

A new clustering method for building multiple trees using deep learning [article]

Nadia Tahiri
2019 bioRxiv   pre-print
Here, we show how Machine Learning (ML) models, based on some interesting properties of the Robinson and Foulds topological distance, can be used to partition a given set of trees into one (when the data  ...  The output of the traditional tree consensus methods is a unique consensus tree or supertree.  ...  Robinson and Foulds topological distance 59 The Robinson and Foulds (RF) topological distance [9] between two trees is the 60 minimum number of elementary operations (contraction and expansion) of  ... 
doi:10.1101/781252 fatcat:wn3t2ahh2nf4tggfxepy4vbp7u

Evolution of pathogenic and nonpathogenic yeasts mitochondrial genomes inferred by supertrees and supermatrices with divergence estimates based on relaxed molecular clocks [article]

Luciano R. Lopes, Renata C. Ferreira, Fernando Antoneli, Paulo B. Paiva, Marcelo R. S. Briones
2018 bioRxiv   pre-print
We also show that the branching patterns do not differ dramatically in supertrees and supermatrix phylogenies.  ...  Here we present phylogenomic supertrees and supermatrix tree of 46 mitochondrial genomes showing that the loss of complex I predates WGD and occurred independently in the S. cerevisiae group and the fission  ...  RF Supertree was inferred using the Robinson-Foulds algorithm as implemented in the RF program (Bansal et al., 2010) .  ... 
doi:10.1101/486944 fatcat:tl7z7jlubvfuva4zac2w4ahuii

Computing the Distribution of a Tree Metric [article]

David Bryant, Mike Steel
2008 arXiv   pre-print
The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees.  ...  for twenty years, an algorithm that is explicitly polynomial time has yet to be described for computing this distribution (which is also the distribution of trees around a given tree under the popular Robinson-Foulds  ...  The metric was introduced by Bourque [1] and generalised by Robinson and Foulds [7] .  ... 
arXiv:0810.0868v1 fatcat:kl5ng5xmzve6totijrvxiry32m
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