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Efficiently Computing Arbitrarily-Sized Robinson-Foulds Distance Matrices [chapter]

Seung-Jin Sul, Grant Brammer, Tiffani L. Williams
Lecture Notes in Computer Science  
In this paper, we introduce the HashRF(p, q) algorithm for computing RF matrices of large binary, evolutionary tree collections.  ...  The novelty of our algorithm is that it can be used to compute arbitrarilysized (p × q) RF matrices without running into physical memory limitations.  ...  Robinson-Foulds (RF) Distance The Robinson-Foulds (RF) distance between two trees is the number of bipartitions that differ between them.  ... 
doi:10.1007/978-3-540-87361-7_11 fatcat:ljdw5pmztvdbhddnmtoxwio4ti

Fast Recovery of Evolutionary Trees with Thousands of Nodes

Miklós Csurös
2002 Journal of Computational Biology  
Moreover, for almost all trees, our algorithm achieves the same success probability on polylogarithmic sample sizes.  ...  We present a novel distance-based algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n 2 ) time using O(n) working space.  ...  We evaluated the accuracy of the reconstruction by the Robinson-Foulds error (Robinson and Foulds 1981) RF%, which measures the percentage of misplaced internal edges in the tree.  ... 
doi:10.1089/10665270252935467 pmid:12015882 fatcat:4fafkt3wffcylday7j5fdzfrvy

Tree Shape-based approaches for the Comparative study of Cophylogeny [article]

Mariano Avino, Garway T Ng, YiYing He, Mathias S Renaud, Bradley R Jones, Art FY Poon
2018 bioRxiv   pre-print
Next, we used simulations from this model to evaluate 13 distance metrics between these trees and the host tree, including Robinson-Foulds distance and two kernel distances that we developed for labeled  ...  and unlabeled trees, which use branch lengths and can accommodate trees of different sizes.  ...  The Robinson-Foulds distance (RF; Robinson and Foulds 1981) counts the minimum number of operations required to transform one tree topology to another, given that they relate the same set of taxa.  ... 
doi:10.1101/388116 fatcat:n6g3h6sy7vgstewbxut6o7u3da

Generalised Implementation for Fixed-Length Approximate String Matching under Hamming Distance and Applications

Solon Pissis, Ahmad Retha
2015 2015 IEEE International Parallel and Distributed Processing Symposium Workshop  
MaxShiftM is a bit-parallel algorithm for fixed-length approximate string matching under the Hamming distance model with time complexity O(m h/w n), where w is the size of the computer word (Crochemore  ...  can be used to improve the accuracy and efficiency of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies.  ...  for phylogenetic reconstruction) by computing the pairwise Robinson and Foulds (RF) distance [21] of the inferred trees.  ... 
doi:10.1109/ipdpsw.2015.106 dblp:conf/ipps/PissisR15 fatcat:ttxri4mxtbbdzm5gni6d6p2kra

NCBI's Virus Discovery Codeathon: Building "FIVE" —The Federated Index of Viral Experiments API Index

Joan Martí-Carreras, Alejandro Gener, Sierra Miller, Anderson Brito, Christiam Camacho, Ryan Connor, Ward Deboutte, Cody Glickman, David Kristensen, Wynn Meyer, Sejal Modha, Alexis Norris (+21 others)
2020 Viruses  
Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases.  ...  Robinson-Foulds distance was calculated using the RF.dist function implemented in the Phangorn package [20] .  ...  Robinson-Foulds distance was calculated using the RF.dist function implemented in the Phangorn package [20] .  ... 
doi:10.3390/v12121424 pmid:33322070 fatcat:5bt5obp7wvau5ptgvjnxvdydem

Algorithms for Computing the Triplet and Quartet Distances for Binary and General Trees

Andreas Sand, Morten Holt, Jens Johansen, Rolf Fagerberg, Gerth Brodal, Christian Pedersen, Thomas Mailund
2013 Biology  
These distances can trivially be computed by explicitly enumerating all sets of three or four leaves and testing if the topologies are different, but this leads to time complexities at least of the order  ...  Distance measures between trees are useful for comparing trees in a systematic manner, and several different distance measures have been proposed.  ...  Commonly used distance measures are the Robinson-Foulds distance [1] and the quartet distance [2] for unrooted trees and the triplet distance [3] for rooted trees.  ... 
doi:10.3390/biology2041189 pmid:24833220 pmcid:PMC4009797 fatcat:7ui4trfj75aw3nvunuy7utiquq

Markov katana: a novel method for Bayesian resampling of parameter space applied to phylogenetic trees [article]

Stephen Pollard, Kenji Fukushima, Zhengyuan O Wang, Todd A Castoe, David Pollock
2018 bioRxiv   pre-print
We demonstrate that this method can be used to efficiently estimate a Bayesian posterior.  ...  The evolutionary model used to generate distances in our prototype was far simpler than the more complex model used to evaluate the likelihood of phylogenies based on the full dataset.  ...  Increasing the jump size in general increases the average Robinson-Foulds (RF) distance between jumps and proposals.  ... 
doi:10.1101/250951 fatcat:6qcd3jiszbbu5akjhm4b6xjabu

New Approaches to Phylogenetic Tree Search and Their Application to Large Numbers of Protein Alignments

Simon Whelan, Thomas Buckley
2007 Systematic Biology  
The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies.  ...  I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds.  ...  This is achieved by measuring the minimum Robinson-Foulds (RF) distance (Robinson and Foulds, 1981) between the resampled tree and those already visited and rejecting trees that are within a certain  ... 
doi:10.1080/10635150701611134 pmid:17849327 fatcat:6pb6bz47ljbq5dlsd4stqnaqcq

Estimating the phylogeny of geoemydid turtles (Cryptodira) from landmark data: an assessment of different methods

Eduardo Ascarrunz, Julien Claude, Walter G. Joyce
2019 PeerJ  
analysis under parsimony, traditional Farris parsimony, unweighted squared-change parsimony, maximum likelihood with a Brownian motion model, and neighbour-joining on a matrix of pairwise Procrustes distances  ...  Robinson-Foulds distance tree space).  ...  For this, we computed pairwise distance matrices of all the trees using the quartet distance (Estabrook, McMorris & Meacham, 1985) and the Robinson-Foulds distance, which are closely related to the dQ  ... 
doi:10.7717/peerj.7476 pmid:31497387 pmcid:PMC6708579 fatcat:7jhihrh4gbbulb3kid5qg32obe

A GA for maximum likelihood phylogenetic inference using neighbour-joining as a genotype to phenotype mapping

Leon Poladian
2005 Proceedings of the 2005 conference on Genetic and evolutionary computation - GECCO '05  
Some do not include any information on edge lengths, those that do include the Robinson-Foulds metric [27] and the branch score [18] .  ...  After some trial and error, a population size of 500 and tournament size of 5 was used. Recombination-Mutation Operators Special genetic operators that act on matrices were invented.  ... 
doi:10.1145/1068009.1068076 dblp:conf/gecco/Poladian05 fatcat:rd7juhpe6fbzzoqlqolcgf73l4

Phylogenomic subsampling and the search for phylogenetically reliable loci [article]

Nicolás Mongiardino Koch
2021 bioRxiv   pre-print
This step is often motivated by either computational limitations associated with the use of complex inference methods, or as a means of testing the robustness of phylogenetic results by discarding loci  ...  Among these are two widely employed proxies for phylogenetic 408 signal: the Robinson-Foulds (RF) similarity to the species tree (i.e., the complement of the RF distance; 409 Robinson and Foulds 1981),  ...  frequency variability 133 (RCFV; Nesnidal, et al. 2010) ; 11) average BS support; 12) Robinson-Foulds (RF) similarity to the 134 species tree supported by each study (Robinson and Foulds 1981) ; two  ... 
doi:10.1101/2021.02.13.431075 fatcat:4thnpvgfcrd3bbcosytjrd3ll4

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time [chapter]

Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
2011 Lecture Notes in Computer Science  
In computational phylogenetics, supertree methods provide a way to reconstruct larger clades of the Tree of Life.  ...  In this paper, we present a novel approach for the computation of supertrees called FlipCut supertree.  ...  We use the Robinson-Foulds (RF) distance and the MAST distance. Results are shown in Fig. 4 and 5.  ... 
doi:10.1007/978-3-642-22685-4_4 fatcat:mfn33nqqcbay5cyeuwxkwwhebi

FlipCut Supertrees: Towards Matrix Representation Accuracy in Polynomial Time

Malte Brinkmeyer, Thasso Griebel, Sebastian Böcker
2012 Algorithmica  
In computational phylogenetics, supertree methods provide a way to reconstruct larger clades of the Tree of Life.  ...  In this paper, we present a novel approach for the computation of supertrees called FlipCut supertree.  ...  We use the Robinson-Foulds (RF) distance and the MAST distance. Results are shown in Fig. 4 and 5.  ... 
doi:10.1007/s00453-012-9698-3 fatcat:wdzdf6z4trbincodqoqg2pshym

Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

Leonardo de Oliveira Martins, Élcio Leal, Hirohisa Kishino, Mark Isalan
2008 PLoS ONE  
We developed a distance measure between unrooted topologies that closely resembles the number of recombinations.  ...  This recombination distance is related to recombination hotspots. Applying this procedure to a genomic HIV-1 dataset, we found evidence for hotspots and de novo recombination.  ...  The cMAST estimates (black) were calculated with PAUP [33] , while the Robinson-Foulds (RF) distance (gray) and our d SPR approximation (blue) were computed using in-house software.  ... 
doi:10.1371/journal.pone.0002651 pmid:18612422 pmcid:PMC2440540 fatcat:6nf2sa27ovamvnp6wxjs6b3vri

Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

Frederick A. Matsen IV, Steven N. Evans, Ahmed Moustafa
2013 PLoS ONE  
Moreover, the length of an edge is a suitably defined distance between the averaged samples associated with the two incident nodes, rather than the less interpretable average of distances produced by UPGMA  ...  The Robinson-Foulds (RF) metric [30] of two trees T and S was computed as half the size of the symmetric difference of the splitset of T and that of S.  ...  We call the resulting quantity the rooted Robinson-Foulds distance. For a bifurcating tree on six leaves such as C, the maximal rooted RF distance is four.  ... 
doi:10.1371/journal.pone.0056859 pmid:23505415 pmcid:PMC3594297 fatcat:jpdgeul32vb7jlnwabvgjid46e
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