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On the Linear-Cost Subtree-Transfer Distance between Phylogenetic Trees

B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp
1999 Algorithmica  
Computing the linear-cost subtree-transfer distance between two w eighted phylogenetic trees is NP-hard, provided we a l l o w m ultiple leaves of a tree to share the same label (i.e. the trees are not  ...  The linear-cost subtree-transfer distance is in fact identical to the nni distance on unweighted phylogenies. 2.  ...  Hein for explaining to us the biological motivations for comparing weighted phylogenies and studying the linear-cost subtree-transfer distance, respectively, T akashi Yokomori, Shengke Y u, and Louxin  ... 
doi:10.1007/pl00008273 fatcat:a55jxp6dofbw3eh56vdrqpcoue

Page 6727 of Mathematical Reviews Vol. , Issue 2000i [page]

2000 Mathematical Reviews  
[Tromp, John] (NL-MATH; Amsterdam) On the linear-cost subtree-transfer distance between phylogenetic trees. (English summary) Algorithmica 25 (1999), no. 2-3, 176-195.  ...  The linear-cost subtree-transfer distance is in fact identical to the nni distance on unweighted phylogenies. 2.  ... 

Nearest Neighbor Interchange and Related Distances [chapter]

Bhaskar DasGupta, Xin He, Ming Li, John Tromp, Louxin Zhang
2014 Encyclopedia of Algorithms  
However, both unicast/multicast routing game and multicast cost sharing game are one folded: the unicast/multicast routing game does not take the receivers into account while the multicast cost sharing  ...  The first and foremost, the upper bound and lower bound on˛still have a gap of r if the multicast system is˛-stable; and a gap of 2r if the multicast system is˛-Nash stable.  ...  2-approximation algorithm for the linear-cost subtree-transfer distance on weighted evolutionary trees.  ... 
doi:10.1007/978-3-642-27848-8_256-2 fatcat:hz7j6d44praz5ef4w62q6dcrya

Nearest Neighbor Interchange and Related Distances [chapter]

Bhaskar DasGupta, Xin He, Ming Li, John Tromp, Louxin Zhang
2016 Encyclopedia of Algorithms  
However, both unicast/multicast routing game and multicast cost sharing game are one folded: the unicast/multicast routing game does not take the receivers into account while the multicast cost sharing  ...  The first and foremost, the upper bound and lower bound on˛still have a gap of r if the multicast system is˛-stable; and a gap of 2r if the multicast system is˛-Nash stable.  ...  2-approximation algorithm for the linear-cost subtree-transfer distance on weighted evolutionary trees.  ... 
doi:10.1007/978-1-4939-2864-4_256 fatcat:baryoj74szfutnczeqpjq2ttw4

Nearest Neighbor Interchange and Related Distances [chapter]

Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Louxin Zhang
2008 Encyclopedia of Algorithms  
However, both unicast/multicast routing game and multicast cost sharing game are one folded: the unicast/multicast routing game does not take the receivers into account while the multicast cost sharing  ...  The first and foremost, the upper bound and lower bound on˛still have a gap of r if the multicast system is˛-stable; and a gap of 2r if the multicast system is˛-Nash stable.  ...  2-approximation algorithm for the linear-cost subtree-transfer distance on weighted evolutionary trees.  ... 
doi:10.1007/978-0-387-30162-4_256 fatcat:45i6bhsce5dx3mfkzmdwt6m2oi

High Performance Phylogenetic Analysis With Maximum Parsimony on Reconfigurable Hardware

Server Kasap, Khaled Benkrid
2011 IEEE Transactions on Very Large Scale Integration (vlsi) Systems  
The hardware architecture consists in a linear systolic array composed of 20 processing elements each of which performing Sankoff's algorithm for a different tree topology in parallel.  ...  We present in this paper the detailed field-programmable gate-array (FPGA) design of the Maximum Parsimony method for molecular-based phylogenetic analysis and its implementation on the nodes of an FPGA  ...  There are various cost schemes which can be represented as a cost matrix that assigns a cost for the change between each pair of character states.  ... 
doi:10.1109/tvlsi.2009.2039588 fatcat:pkegv7vzajh2xkkoxc327z3owu

A high performance FPGA-based core for phylogenetic analysis with Maximum Parsimony method

Server Kasap, Khaled Benkrid
2009 2009 International Conference on Field-Programmable Technology  
We present in this paper the detailed FPGA design of the Maximum Parsimony method for molecular-based phylogenetic analysis and its implementation on a Xilinx Virtex-4 FPGA chip.  ...  The hardware architecture consists of a linear systolic array composed of 20 processing elements each of which performing the Sankoff's algorithm for a different tree topology in parallel.  ...  There are various cost schemes which can be represented as a cost matrix that assigns a cost for the change between each pair of character states.  ... 
doi:10.1109/fpt.2009.5377652 fatcat:mpec4zmpejbmvlmetletnzzeam

A reconstruction problem for a class of phylogenetic networks with lateral gene transfers

Gabriel Cardona, Joan Carles Pons, Francesc Rosselló
2015 Algorithms for Molecular Biology  
, and a set of extra secondary arcs between nodes in this tree representing lateral gene transfers.  ...  We then give an algorithm that, given a set of pairwise different phylogenetic trees T 0 , T 1 , . . . , T k on the same set of taxa, outputs, when it exists, the LGT network that satisfies these conditions  ...  Acknowledgements We thank the anonymous reviewers for many comments and suggestions that have substantially improved the quality and readability of the paper.  ... 
doi:10.1186/s13015-015-0059-z pmid:26691555 pmcid:PMC4683721 fatcat:753gdv5lfzgvlnd4prmo5oztku

Scatter search with path relinking for phylogenetic inference

Carlos Cotta
2006 European Journal of Operational Research  
method based on internal rotations of subtrees.  ...  We propose the use of scatter search with path relinking for the inference of phylogenetic trees. Solutions are here represented as trees whose leaves span the set of species under study.  ...  Thanks are due to the anonymous reviewers for their detailed comments, and to Dr. Moscato for continuous (and compelling) discussions on bioinformatics.  ... 
doi:10.1016/j.ejor.2004.08.013 fatcat:jn4jyhobsjhvrfb3mcqjtr5kfq

Rapidly Computing the Phylogenetic Transfer Index [article]

Jakub Michal Truszkowski, Olivier Gascuel, Krister Swenson
2019 biorxiv/medrxiv   pre-print
Given trees T and T_o on the same taxon set, the transfer index φ(b, T_o ) is the number of taxa that need to be ignored so that the bipartition induced by branch b in T is equal to some bipartition in  ...  Recently, Lemoine et al. [13] used the transfer index to design a novel bootstrap analysis technique that improves on Felsenstein bootstrap on large, noisy data sets.  ...  First, we initialize the D values by computing the rooted transfer distance from the empty subtree to every subtree in T o .  ... 
doi:10.1101/743948 fatcat:nagponaznfbxpf6p2m7h4soikq

Inference of a Phylogenetic Tree: Hierarchical Clustering versus Genetic Algorithm [chapter]

Glenn Blanchette, Richard O'Keefe, Lubica Benuskova
2012 Lecture Notes in Computer Science  
This paper compares the implementations and performance of two computational methods, hierarchical clustering and a genetic algorithm, for inference of phylogenetic trees in the context of the artificial  ...  For a small problem space of the original species proposed by Camin (1965) the genetic algorithm was able to produce a solution which had a lower Fitch cost and was closer to the theoretical evolution  ...  Introduction Phylogenetic trees are a diagrammatic representation of the evolutionary relationships between taxonomic units (TU).  ... 
doi:10.1007/978-3-642-35101-3_26 fatcat:tbo5gdiz7jfyvjlqcmn5an36wy

Codivergence of Mycoviruses with Their Hosts

Markus Göker, Carmen Scheuner, Hans-Peter Klenk, J. Benjamin Stielow, Wulf Menzel, David M. Ojcius
2011 PLoS ONE  
Additionally, we assessed the sensitivity of the co-phylogenetic tests to the settings for inferring virus trees from their genome sequences and approximate, taxonomy-based host trees.  ...  This is the first study of mycovirus-host codivergence, and the results shed light not only on how mycovirus biology affects their co-phylogenetic relationships, but also on their presumable host range  ...  Hence, one might interpret the congruence between mycovirus and host phylogenies as indicative of a little probability of lateral transfer between hosts, based on the assumption that otherwise resource  ... 
doi:10.1371/journal.pone.0022252 pmid:21829452 pmcid:PMC3146478 fatcat:zrxzoqrg5jgxvcjjmbkvkykrgy

Efficient Parallel Computation of Nearest Neighbor Interchange Distances [article]

Mikael Gast, Mathias Hauptmann
2012 arXiv   pre-print
The nni-distance is a well-known distance measure for phylogenetic trees.  ...  Given two phylogenetic trees T1 and T2 on the same set of taxa and with the same multi-set of edge-weights, the algorithm constructs a sequence of nni-operations of weight at most O(log n) \cdot opt, where  ...  Furthermore, they observed that the nni-distance is identical to the linear-cost subtree-transfer distance on unweighted phylogenies [DHJ + 99] and gave an outline of an exact algorithm for distance-restricted  ... 
arXiv:1205.3402v1 fatcat:phher3pgmbexjbx6hefdrlsbaq

Scalable Phylogenetics through Input Preprocessing [chapter]

Roberto Blanco, Elvira Mayordomo, Esther Montes, Rafael Mayo, Angelines Alberto
2010 Advances in Intelligent and Soft Computing  
Phylogenetic reconstruction is one of the fundamental problems in computational biology.  ...  The combinatorial explosion of the state space and the complexity of mathematical models impose practical limits on workable problem sizes.  ...  Roberto Blanco was supported by Grant AP2008-03447 from the Spanish Ministry of Education.  ... 
doi:10.1007/978-3-642-13214-8_16 dblp:conf/isami/BlancoMMMA10 fatcat:atkuqzli6jgdxgw4tpdxwmmlwu

MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers [article]

Cedric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely Szollosi, Vincent Daubin, Eric Tannier
2017 bioRxiv   pre-print
When a set of transfers is detected by interpreting the phylogenetic discordance between gene trees and a species tree, the set of all deduced time constraints can be used to rank the species tree, {\em  ...  In most conditions the obtained ranked tree is very close to the real one, confirming the potential of dating the history of life with transfers by maximizing time consistency.  ...  1 , S r 2 ) is the Kendall distance between the two ranked trees.  ... 
doi:10.1101/127548 fatcat:f4lwbd4arrh3ljgl2hf5oyyuze
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