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QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS

PHILIPPE GAMBETTE, VINCENT BERRY, CHRISTOPHE PAUL
<span title="">2012</span> <i title="World Scientific Pub Co Pte Lt"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zudjdcas3bcm3lfnfxnjyl5zty" style="color: black;">Journal of Bioinformatics and Computational Biology</a> </i> &nbsp;
We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks.  ...  In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks.  ...  We also thank Steven Kelk and anonymous referees whose comments helped to improve this paper.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720012500047">doi:10.1142/s0219720012500047</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22809417">pmid:22809417</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mwldjejgrrgvlldpiwrw4j6ut4">fatcat:mwldjejgrrgvlldpiwrw4j6ut4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190417003402/https://core.ac.uk/download/pdf/48341839.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/2a/d92a925681ed7625a3baaa10db9d3f820f53f27e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/s0219720012500047"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

The Tree of Blobs of a Species Network: Identifiability under the Coalescent [article]

Elizabeth S. Allman, Hector Baños, Jonathan D. Mitchell, John A. Rhodes
<span title="2022-05-06">2022</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
An identifiability theorem, that most features of the unrooted tree of blobs can be determined from the distribution of gene quartet topologies, is established.  ...  Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands.  ...  Roger and Edward Susko.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2205.03466v1">arXiv:2205.03466v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fuq2kpgsszfoppu32qvdkgckju">fatcat:fuq2kpgsszfoppu32qvdkgckju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220512221405/https://arxiv.org/pdf/2205.03466v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c1/5c/c15c485deb19c09cddc22d085439e6256e230f8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2205.03466v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Identifying Species Network Features from Gene Tree Quartets Under the Coalescent Model

Hector Baños
<span title="2018-08-09">2018</span> <i title="Springer Nature America, Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zasl75vjunffjdn7osabykmsua" style="color: black;">Bulletin of Mathematical Biology</a> </i> &nbsp;
We show additionally how to compute quartet concordance factors for a network in terms of simpler networks, and explore some circumstances in which cycles of size 3 and hybrid nodes in 4cycles can be detected  ...  We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model.  ...  Rhodes and Elizabeth S. Allman for their technical assistance and suggestions during the development of this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11538-018-0485-4">doi:10.1007/s11538-018-0485-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30094772">pmid:30094772</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/quzb7elclvguxnflunhwgfo6vq">fatcat:quzb7elclvguxnflunhwgfo6vq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307093454/http://pdfs.semanticscholar.org/f71b/f8fa9012a74db693adad01c138638de18cae.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f7/1b/f71bf8fa9012a74db693adad01c138638de18cae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11538-018-0485-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Identifying species network features from gene tree quartets under the coalescent model [article]

Hector Baños
<span title="2017-11-28">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We show additionally how to compute quartet concordance factors for a network in terms of simpler networks, and explore some circumstances in which cycles of size 3 and hybrid nodes in 4-cycles can be  ...  We show that many topological features of level-1 species networks are identifiable from the distribution of the gene tree quartets under the network multi-species coalescent model.  ...  Rhodes and Elizabeth S. Allman for their technical assistance and suggestions during the development of this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1711.10545v1">arXiv:1711.10545v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fzhhovaoandipet2cffbpsd4wa">fatcat:fzhhovaoandipet2cffbpsd4wa</a> </span>
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Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

Claudia Solís-Lemus, Cécile Ané, Scott Edwards
<span title="2016-03-07">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development.  ...  Our work makes it possible to learn large phylogenetic networks from large data sets, with a statistical approach and a biologically relevant model.  ...  Stenz for helping with the CF estimation pipeline, Ray Cui for providing MrBayes output of their original analysis, Sarah Friedrich for her help with artwork, David Baum for many meaningful discussions and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1005896">doi:10.1371/journal.pgen.1005896</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26950302">pmid:26950302</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4780787/">pmcid:PMC4780787</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k7bkiiop6jbtzcqequnx5guluy">fatcat:k7bkiiop6jbtzcqequnx5guluy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015095118/http://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1005896&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/63/e663b7aaf9bdd6e99b3817fd3dff3a00e116b070.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1005896"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780787" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NANUQ: a method for inferring species networks from gene trees under the coalescent model

Elizabeth S. Allman, Hector Baños, John A. Rhodes
<span title="2019-12-06">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/izdyn6hngbd35czi6err6qypqu" style="color: black;">Algorithms for Molecular Biology</a> </i> &nbsp;
to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph.  ...  Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters  ...  Authors' contributions All authors contributed equally in the development of the theory, implementation of the algorithm, and manuscript writing. All authors read and approved the final manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13015-019-0159-2">doi:10.1186/s13015-019-0159-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31827592">pmid:31827592</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6896299/">pmcid:PMC6896299</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q7u7b4e2xzgwdlvblzy6sdmd3y">fatcat:q7u7b4e2xzgwdlvblzy6sdmd3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191208153220/https://almob.biomedcentral.com/track/pdf/10.1186/s13015-019-0159-2" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/87/2c/872c7860a3328ab49300f6eb6e75588214a90367.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13015-019-0159-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896299" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NANUQ: A method for inferring species networks from gene trees under the coalescent model [article]

Elizabeth Allman and Hector Banos and John Rhodes
<span title="2019-05-16">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph.  ...  Under the Network Multispecies Coalescent Model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters  ...  Acknowledgements This research was supported, in part, by the National Institutes of Health Grant R01 GM117590, awarded under the Joint DMS/NIGMS Initiative to Support Research at the Interface of the Biological and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1905.07050v1">arXiv:1905.07050v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hsok6oln6fbkvgvn75gzsiy7ji">fatcat:hsok6oln6fbkvgvn75gzsiy7ji</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200828142852/https://arxiv.org/pdf/1905.07050v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/06/ce/06ce9253768723871cb91cbc71eea90ecab1a247.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1905.07050v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting [article]

Claudia Solís-Lemus, Cécile Ané
<span title="2016-02-12">2016</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development.  ...  Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework.  ...  Stenz for helping with the CF estimation pipeline, Ray Cui for providing MrBayes output of their original analysis, Sarah Friedrich for her help with artwork, David Baum for many meaningful discussions and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1509.06075v3">arXiv:1509.06075v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xqib7ri5rzhchiwjqrgsvd76na">fatcat:xqib7ri5rzhchiwjqrgsvd76na</a> </span>
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Tree-like reticulation networks—When do tree-like distances also support reticulate evolution?

Andrew R. Francis, Mike Steel
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hdsimelqbzfw3kuyyukmkz24gq" style="color: black;">Mathematical Biosciences</a> </i> &nbsp;
We consider two types of reticulation networks: hybridisation networks and HGT networks.  ...  Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree.  ...  The first author thanks the Australian Research Council (via FT100100898) and the second author thanks the NZ Marsden Fund and Allan Wilson Centre for helping to fund this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.mbs.2014.10.008">doi:10.1016/j.mbs.2014.10.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25447812">pmid:25447812</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hhgqsjhjezejxl63dk4c3vwbtu">fatcat:hhgqsjhjezejxl63dk4c3vwbtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170429074720/http://www.math.canterbury.ac.nz/%7Em.steel/Non_UC/files/research/arxiv_reticulate.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/35/4e/354e396aa2007f2f56e2a1d6e6e3d90fca608e17.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.mbs.2014.10.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution? [article]

Andrew R. Francis, Mike Steel
<span title="2014-09-23">2014</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We consider two types of reticulation networks: hybridization networks and HGT networks.  ...  Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree.  ...  The first author thanks the Australian Research Council (via FT100100898) and the second author thanks the NZ Marsden Fund and Allan Wilson Centre for helping to fund this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1405.2965v2">arXiv:1405.2965v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/khdmbvz7ubfndiixilsadej2ze">fatcat:khdmbvz7ubfndiixilsadej2ze</a> </span>
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Constructing Optimal Trees from Quartets

David Bryant, Mike Steel
<span title="">2001</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/anp7kqfyerdljfxydqb4objj6a" style="color: black;">Journal of Algorithms</a> </i> &nbsp;
We present applications of this algorithm to a number of problems in phylogenetics, including sequence analysis, construction of trees from phylogenetic networks, and consensus methods.  ...  We present fast new algorithms for constructing phylogenetic trees from quartets (resolved trees on four leaves).  ...  Research supported in part by the Natural Sciences and Engineering Research Council of Canada and the Canadian Genome Analysis and Technology grants to D. Sankoff.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jagm.2000.1133">doi:10.1006/jagm.2000.1133</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x3g3mnbb6vbapi3oui26entabu">fatcat:x3g3mnbb6vbapi3oui26entabu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150117143703/http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/j_alg2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2d/99/2d99c7eb9faea7c887655d180fe82175f6983a5b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jagm.2000.1133"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Phylogenetic incongruence through the lens of Monadic Second Order logic [article]

Steven Kelk, Leo van Iersel, Celine Scornavacca
<span title="2015-03-01">2015</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Many of these measures are NP-hard to compute and this has stimulated a considerable volume of research into fixed parameter tractable algorithms.  ...  Within the field of phylogenetics there is growing interest in measures for summarising the dissimilarity, or 'incongruence', of two or more phylogenetic trees.  ...  A rooted phylogenetic network (rooted network for short) N = (V (N ), E(N )) on a set of taxa X is any rooted acyclic digraph in which no vertex has degree 2 (except possibly the root) and whose leaves  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1503.00368v1">arXiv:1503.00368v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ie42fw4m5nenrhjdmbeh56kqga">fatcat:ie42fw4m5nenrhjdmbeh56kqga</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200928103600/https://arxiv.org/pdf/1503.00368v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/65/41/65410b6c3964afb5548532bc78b3736373efd8ab.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1503.00368v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

New Reduction Rules for the Tree Bisection and Reconnection Distance

Steven Kelk, Simone Linz
<span title="2020-07-01">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b2ajpip3sjhohgv677sfgijhfu" style="color: black;">Annals of Combinatorics</a> </i> &nbsp;
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  ...  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  ...  This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and repro-  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00026-020-00502-7">doi:10.1007/s00026-020-00502-7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xlpy4grmsnaqtj3ypsxgum3mfy">fatcat:xlpy4grmsnaqtj3ypsxgum3mfy</a> </span>
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New reduction rules for the tree bisection and reconnection distance [article]

Steven Kelk, Simone Linz
<span title="2020-06-14">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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  ...  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  ...  Unrooted phylogenetic trees and networks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1905.01468v2">arXiv:1905.01468v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jqtd42o6mvhz7na6gnlm4qdora">fatcat:jqtd42o6mvhz7na6gnlm4qdora</a> </span>
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A Survey of Combinatorial Methods for Phylogenetic Networks

Daniel H. Huson, Celine Scornavacca
<span title="2010-11-15">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/c3tk2qca4vdq5htca2effydqim" style="color: black;">Genome Biology and Evolution</a> </i> &nbsp;
Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal  ...  In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are  ...  In the computation of an unrooted tree or split network, these are phylogenetic trees on sets of four taxa, sometimes called ''quartet trees.''  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gbe/evq077">doi:10.1093/gbe/evq077</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21081312">pmid:21081312</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3017387/">pmcid:PMC3017387</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gspgmsuxuvguhjqfxhsxcduqmm">fatcat:gspgmsuxuvguhjqfxhsxcduqmm</a> </span>
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