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Reflections on kernelizing and computing unrooted agreement forests [article]

Rim van Wersch, Steven Kelk, Simone Linz, Georgios Stamoulis
2021 arXiv   pre-print
Here we explore the practical impact of kernelization (i.e. data reduction) on the NP-hard problem of computing the TBR distance between two unrooted binary phylogenetic trees.  ...  This problem is better-known in the literature as the maximum agreement forest problem, where the goal is to partition the two trees into a minimum number of common, non-overlapping subtrees.  ...  Alhazmi for useful conversations on the topic of this paper and an anonymous referee for their helpful comments.  ... 
arXiv:2012.07354v2 fatcat:jo3g2xy5snge5m3xba5ziig4ty

New Reduction Rules for the Tree Bisection and Reconnection Distance

Steven Kelk, Simone Linz
2020 Annals of Combinatorics  
The new rules combine the "unrooted generator" approach introduced in Kelk and Linz (SIAM J Discrete Math 33(3):1556-1574, 2019) with a careful analysis of agreement forests to identify (i) situations  ...  Recently it was shown that, if the subtree and chain reduction rules have been applied exhaustively to two unrooted phylogenetic trees, the reduced trees will have at most 15k − 9 taxa where k is the TBR  ...  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and repro-  ... 
doi:10.1007/s00026-020-00502-7 fatcat:xlpy4grmsnaqtj3ypsxgum3mfy

New reduction rules for the tree bisection and reconnection distance [article]

Steven Kelk, Simone Linz
2020 arXiv   pre-print
The new rules combine the "unrooted generator" approach introduced in [Kelk and Linz 2018] with a careful analysis of agreement forests to identify (i) situations when chains of length 3 can be further  ...  Recently it was shown that, if the subtree and chain reduction rules have been applied exhaustively to two unrooted phylogenetic trees, the reduced trees will have at most 15k-9 taxa where k is the TBR  ...  Again, let F be an agreement forest for two unrooted binary phylogenetic trees T and T on X, and let C = ( 1 , 2 , . . . , n ) be a common n-chain of T and T .  ... 
arXiv:1905.01468v2 fatcat:jqtd42o6mvhz7na6gnlm4qdora

Deep kernelization for the Tree Bisection and Reconnnect (TBR) distance in phylogenetics [article]

Steven Kelk, Simone Linz, Ruben Meuwese
2022 arXiv   pre-print
Our results also apply to the equivalent problem of computing a Maximum Agreement Forest (MAF) between two unrooted binary phylogenetic trees.  ...  We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees.  ...  Acknowledgements Steven Kelk and Simone Linz were supported by the New Zealand Marsden Fund.  ... 
arXiv:2206.04451v1 fatcat:fupdzicg7ve67nqwxkytaguj5a

Parameterized Algorithms in Bioinformatics: An Overview

Laurent Bulteau, Mathias Weller
2019 Algorithms  
Bioinformatics regularly poses new challenges to algorithm engineers and theoretical computer scientists.  ...  We cover sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics.  ...  Finally, we thank the anonymous reviewers for their helpful and productive comments. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/a12120256 fatcat:4dhjdnpibzh43iifgan2fu6bwa

A tight kernel for computing the tree bisection and reconnection distance between two phylogenetic trees [article]

Steven Kelk, Simone Linz
2019 arXiv   pre-print
Here we reanalyse Allen and Steel's kernelization algorithm and prove that the reduced instances will in fact have at most 15k-9 taxa.  ...  In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where k is the TBR (Tree Bisection  ...  , SPR distance [4, 6, 32] , hybridization number [7, 29, 30] and agreement forests [24, 31] , for example.  ... 
arXiv:1811.06892v2 fatcat:b6zggsuoqjccrf6kywnp2jbiva

Treewidth distance on phylogenetic trees [article]

Steven Kelk, Georgios Stamoulis, Taoyang Wu
2017 arXiv   pre-print
On a slightly different note we show that if a display graph is formed from the fusion of a phylogenetic network and a tree, rather than from two trees, the treewidth of the display graph is bounded whenever  ...  We also show that the gap between treewidth and Tree Bisection and Reconnect (TBR) distance can be infinitely large, and that unlike, for example, planar graphs the treewidth of the display graph can be  ...  Computing the TBR-distance is essentially equivalent to the Maximum Agreement Forest (MAF) problem: Given an unrooted binary phylogenetic tree on X and X ⊂ X we let T (X ) denote the minimal subtree that  ... 
arXiv:1703.10840v1 fatcat:n7plhael4nblnker7xmmxe5npe

Sharp upper and lower bounds on a restricted class of convex characters [article]

Steven Kelk, Ruben Meuwese
2021 arXiv   pre-print
Finally, we reflect briefly on possible algorithmic applications of these results.  ...  Let 𝒯 be an unrooted binary tree with n distinctly labelled leaves.  ...  There are many convex characters that do not induce agreement forests, butcrucially -every agreement forest does induce a convex character.  ... 
arXiv:2107.10871v1 fatcat:3rzjketgfvhmjbuw4x4tlbk6m4

Sharp Upper and Lower Bounds on a Restricted Class of Convex Characters

Steven Kelk, Ruben Meuwese
2022 Electronic Journal of Combinatorics  
Finally, we reflect briefly on possible algorithmic applications of these results.  ...  Let $\mathcal{T}$ be an unrooted binary tree with $n$ distinctly labelled leaves.  ...  Acknowledgements Ruben Meuwese was supported by the Dutch Research Council (NWO) KLEIN 1 grant Deep kernelization for phylogenetic discordance, project number OCENW.KLEIN.305.  ... 
doi:10.37236/10589 fatcat:ue5nekc6tnebjpimxycgancsgi

Treewidth of display graphs: bounds, brambles and applications

Remie Janssen, Mark Jones, Steven Kelk, Georgios Stamoulis, Taoyang Wu
2019 Journal of Graph Algorithms and Applications  
We conclude with a discussion on the future use of display graphs and treewidth in phylogenetics.  ...  Here we further elucidate the properties of display graphs and their interaction with treewidth.  ...  Acknowledgements Mark Jones and Remie Janssen were supported by Leo van Iersel's Vidi grant (NWO): 639.072.602. Georgios Stamoulis was supported by an NWO TOP  ... 
doi:10.7155/jgaa.00508 fatcat:hy7gfl4umjbm7pxx2ojwwfofla

Hybridization Number on Three Rooted Binary Trees is EPT

Leo van Iersel, Steven Kelk, Nela Lekić, Chris Whidden, Norbert Zeh
2016 SIAM Journal on Discrete Mathematics  
The connection to acyclic agreement forests is much weaker for more than two trees, so even given the right agreement forest, the reconstruction of the network poses major challenges.  ...  We present an algorithm for the hybridization number problem on three binary phylogenetic trees on n leaves that runs in time O(c k poly(n)) with k the hybridization number of an optimal network and c  ...  problem and the maximum acyclic agreement forest (MAAF) problem.  ... 
doi:10.1137/15m1036579 fatcat:zdfqmpl3gzgxlo7sol3kmgn7li

Universal Pacemaker of Genome Evolution

Sagi Snir, Yuri I. Wolf, Eugene V. Koonin, Berend Snel
2012 PLoS Computational Biology  
We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in  ...  the evolution of archaea and bacteria and that were constrained according to the two models.  ...  Acknowledgments We thank Pere Puigbo and Natalya Yutin for generous help with handling the phylogenetic trees. Author Contributions Conceived and designed the experiments: SS YIW EVK.  ... 
doi:10.1371/journal.pcbi.1002785 pmid:23209393 pmcid:PMC3510094 fatcat:y5cjuk7lmrdexfcwepuffzkt64

A Survey of Graph Mining Techniques for Biological Datasets [chapter]

S. Parthasarathy, S. Tatikonda, D. Ucar
2010 Managing and Mining Graph Data  
We conclude this article with a discussion of the key results and identify some interesting directions for future research.  ...  In this article we survey the principal results in the field examining them both from the algorithmic contributions and applicability in the domain in question.  ...  After all the kernels are identified, nodes that are not part of any kernels are further analyzed and the ones that are similar to any of the kernels are included into the kernel and the kernel's fingerprint  ... 
doi:10.1007/978-1-4419-6045-0_18 dblp:series/ads/ParthasarathyTU10 fatcat:aeu53r3dbzd67d5whkjypv64uq

Pollutants and Insecticides Drive Local Adaptation in African Malaria Mosquitoes

Colince Kamdem, Caroline Fouet, Stephanie Gamez, Bradley J. White
2017 Molecular biology and evolution  
Importantly, in both species, rural and urban populations are genetically differentiated. Genome scans reveal pervasive signatures of selection centered on genes involved in xenobiotic resistance.  ...  We find evidence for genetic and geographic subdivision within An. coluzzii and An. gambiae sensu stricto-the two most significant malaria vectors in the region.  ...  This work would not have been possible without the collaboration of inhabitants and administrative authorities of all sampled sites and we want to underscore their generosity and patience.  ... 
doi:10.1093/molbev/msx087 pmid:28204524 pmcid:PMC5400387 fatcat:ymejstjrzbfexiztiye2eo77gy

Machine learning substantiates biologically meaningful species delimitations in the phylogenetically complex North American box turtle genus Terrapene [article]

Bradley T. Martin, Tyler K. Chafin, Marlis R. Douglas, John S. Placyk, Roger D. Birkhead, Chris A. Phillips, Michael E. Douglas
2020 bioRxiv   pre-print
First, more traditional model-based approaches perform poorly, a likely reflection of systematic biases inherent in their formulation.  ...  Model-based approaches to species delimitation are constrained both by computational capacities as well as by algorithmic assumptions that are frequently violated when applied to biologically complex systems  ...  Pummill, and Z.  ... 
doi:10.1101/2020.05.19.103598 fatcat:hinius3tqzhtdhyybjvsqif5ni
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