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Inferring evolutionary trees with strong combinatorial evidence [chapter]

Vincent Berry, Olivier Gascuel
<span title="">1997</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
We propose a quartet reconstruction method which speciÿcally produces trees whose edges have strong combinatorial evidence.  ...  We consider the problem of inferring the evolutionary tree of a set of n species.  ...  We investigate here a phylogenetic reconstruction method which speciÿcally produces trees whose edges have a strong combinatorial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bfb0045078">doi:10.1007/bfb0045078</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wdyexuu7lvh47cskdffltpd4zq">fatcat:wdyexuu7lvh47cskdffltpd4zq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923230953/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/093/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDMwNDM5NzU5OTAwMjM1Mg%3D%3D.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/aa/16/aa16f13e3a49c4470bfac654e1bc82e6acb5e9f7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bfb0045078"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Inferring evolutionary trees with strong combinatorial evidence

Vincent Berry, Olivier Gascuel
<span title="">2000</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/elaf5sq7lfdxfdejhkqbtz6qoq" style="color: black;">Theoretical Computer Science</a> </i> &nbsp;
We propose a quartet reconstruction method which speciÿcally produces trees whose edges have strong combinatorial evidence.  ...  We consider the problem of inferring the evolutionary tree of a set of n species.  ...  We investigate here a phylogenetic reconstruction method which speciÿcally produces trees whose edges have a strong combinatorial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0304-3975(99)00235-2">doi:10.1016/s0304-3975(99)00235-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3ct56ylc7rc4tbjfyictkv5g3u">fatcat:3ct56ylc7rc4tbjfyictkv5g3u</a> </span>
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Page 4383 of Mathematical Reviews Vol. , Issue 99f [page]

<span title="">1999</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
John Haigh (4-SUSX; Brighton) 99f:92011 92D15 68Q25 Berry, Vincent (F-MONT2-FI; Montpellier) ; Gascuel, Olivier (3-MTRLC-G; Montreal, PQ) Inferring evolutionary trees with strong combinatorial evidence  ...  We propose a quartet reconstruction method which specifically produces trees whose edges have strong combinatorial evidence. For this purpose we use the Q* relation {H.-J. Bandelt and A. W. M.  ... 
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Page 3617 of Mathematical Reviews Vol. , Issue 2000e [page]

<span title="">2000</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Press, Los Alamitos, CA, 1993; MR 95k:68059] have provided strong evidence that the VC-dimension decision problem is not in P.  ...  Provided the r points are chosen indepen- dently from the same (unknown, arbitrary) distribution, the target rectangle may be inferred with small error in polynomial time.  ... 
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The evolution of tumour phylogenetics: principles and practice

Russell Schwartz, Alejandro A. Schäffer
<span title="2017-02-13">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wg7vnqrxzveutlxxgtyxqydvjy" style="color: black;">Nature reviews genetics</a> </i> &nbsp;
bursts of rapid evolution under strong selection, although this model cannot explain the evidence for a lack of selection in some tumours 48 .  ...  FIGURE 2 provides a simplified overview of the pitfalls in this process, as we seek to infer a true tree (FIG. 2a) but struggle with erroneous inferences induced by a mis match between the evolutionary  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nrg.2016.170">doi:10.1038/nrg.2016.170</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28190876">pmid:28190876</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5886015/">pmcid:PMC5886015</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h2rpqbaxdjfkxdbaj7nlirw6xy">fatcat:h2rpqbaxdjfkxdbaj7nlirw6xy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829202608/http://www.nature.com/nrg/journal/v18/n4/pdf/nrg.2016.170.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/ec/8b/ec8b1a8d47cfae7886f73e10faf3a145cbcca04a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nrg.2016.170"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886015" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PastView: a user-friendly interface to explore evolutionary scenarios [article]

Francois Chevenet, Guillaume Castel, Emmanuelle Jousselin, Olivier Gascuel
<span title="2019-05-27">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios  ...  Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology  ...  "Gene Ontology », any data related to patients), are used and without evidence of a strong structuring of data between tree and annotations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/651661">doi:10.1101/651661</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y7ijpgqxzra5hmkbtl4ewp7k3a">fatcat:y7ijpgqxzra5hmkbtl4ewp7k3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324131311/https://www.biorxiv.org/content/biorxiv/early/2019/05/27/651661.full.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/02/09/0209d8c11e8c4fade274eecde1e0a6a9a55d80fa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/651661"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Page 6830 of Mathematical Reviews Vol. , Issue 2001I [page]

<span title="">2001</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
evolutionary trees with strong combinatorial evidence.  ...  The authors consider the problem of inferring the evolutionary tree (phylogeny) for a set S of n species using quartets.  ... 
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Mathematical approaches to comparative linguistics

T. Warnow
<span title="1997-06-24">1997</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
The inference of the evolutionary history of a set of languages is a complex problem.  ...  Evolutionary History Inference of Related Languages.  ...  the evolutionary tree for the languages.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.94.13.6585">doi:10.1073/pnas.94.13.6585</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11607730">pmid:11607730</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC34482/">pmcid:PMC34482</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u5636dbypfa2hduxbccaoizdlm">fatcat:u5636dbypfa2hduxbccaoizdlm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181030061617/http://www.pnas.org/content/pnas/94/13/6585.full.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/fd/da/fdda61d33cd1f2a225af7d3b020b364d21f3a565.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.94.13.6585"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC34482" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

Minglei Wang, Gustavo Caetano-Anollés
<span title="">2009</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y4oayrlrkfebxgzkm3rrzcps2m" style="color: black;">Structure</a> </i> &nbsp;
These trees defined timelines of architectural discovery and revealed remarkable evolutionary patterns, including the explosive appearance of domain combinations during the rise of organismal lineages,  ...  Protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements.  ...  Phylogenetic congruence over such broad timescales provides strong evidence for a historical association between the architecture of functional proteins and the structure of embedded domains.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.str.2008.11.008">doi:10.1016/j.str.2008.11.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19141283">pmid:19141283</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yz3f3mopmvb7zistfbz4j5wbl4">fatcat:yz3f3mopmvb7zistfbz4j5wbl4</a> </span>
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Analysis of Gene Order Evolution Beyond Single-Copy Genes [chapter]

Nadia El-Mabrouk, David Sankoff
<span title="">2012</span> <i title="Humana Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes?  ...  We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely  ...  In the presence of a strong phylogenetic signal, inferred trees are usually binary, as a speciation event usually results in the creation of two new species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-61779-582-4_15">doi:10.1007/978-1-61779-582-4_15</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22407718">pmid:22407718</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kerbedfsgrgi5npicdlbd6u4aa">fatcat:kerbedfsgrgi5npicdlbd6u4aa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120124164401/http://www.iro.umontreal.ca/~mabrouk/Publications/chapterMMB11.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/64/ee/64ee4f3ac60ec3dc272795414da808ecd68b7ab1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-61779-582-4_15"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Matrilocal residence is ancestral in Austronesian societies

F. M. Jordan, R. D. Gray, S. J. Greenhill, R. Mace
<span title="2009-03-04">2009</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f4dvulqgv5hongx66rijauzrt4" style="color: black;">Proceedings of the Royal Society of London. Biological Sciences</a> </i> &nbsp;
We thank Robert Blust, John Lynch, Jeff Marck, Cordelia Nickelsen, Malcolm Ross, Laurent Sagart and all contributors to the ABVD for their assistance with lexical data and cognate judgements, and BeSTGRID.org  ...  PMP-p K64.99 8.38 strong evidence for matrilocality POC-m K62.79 POC-p K61.50 K2.58 positive evidence for patrilocality equal rates K63.12 default K59.61 K7.03 strong evidence for unequal  ...  Our results (table 1) show that there is strong evidence in favour of PMP matrilocality, positive evidence for PAn matrilocality and positive evidence for POc patrilocality.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspb.2009.0088">doi:10.1098/rspb.2009.0088</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19324748">pmid:19324748</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2677244/">pmcid:PMC2677244</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7yv2mrpvrzevvmtgxlkiiv4u34">fatcat:7yv2mrpvrzevvmtgxlkiiv4u34</a> </span>
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Conservation of Distantly Related Membrane Proteins: Photosynthetic Reaction Centers Share a Common Structural Core

Sumedha Sadekar, Jason Raymond, Robert E. Blankenship
<span title="2006-08-03">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4bimmtjdczetrfmnc3ijbmwpoy" style="color: black;">Molecular biology and evolution</a> </i> &nbsp;
A relationship of sequence with structure was derived from the reaction center structures; with characteristic decay length of 1.6 Å .  ...  All available evidences suggest that the earliest photosynthetic organisms were anoxygenic and that oxygen-evolving photosynthesis is a more recent development.  ...  In addition, we derive sequence alignments and thereby phylogenetic trees based on structure, compare these results with more traditional sequence-based trees, and use the results to make inferences about  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msl079">doi:10.1093/molbev/msl079</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16887904">pmid:16887904</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k7djmfqnhfg6xgiq4vlntbqugu">fatcat:k7djmfqnhfg6xgiq4vlntbqugu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724135036/https://watermark.silverchair.com/msl079.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaMwggGfBgkqhkiG9w0BBwagggGQMIIBjAIBADCCAYUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM6gIWgact6sWX7WEZAgEQgIIBVrxep-TZB27WGGQ8fsr9fa9CfKdyiHPE8R8EcNzm5dC-8kdbGkn_iPeRM1NUT919aPY8HZaHNc8rZTeB0G346NFik3y0USH3y-aDFyutPb-8FujTmpxXk9xXGy7XTR6rqTvC9azohYvLBdjH8vJOLt-PqIzuAyc_TepunwXFE4psvFpK2NCE0BOu4ooO9z-o9VyXxR6NCF_8V0_PhdWDzFfetz6KoDaciXtnNaUm1IRUWYkSMG0rbfAAbF3k10Xw6RvFG0BxHkbP5hGIXd_kydCCl62BXTMUZS6rpGY5MJxZ_EBHxBAnaQYlxVazfyDUW7lEwxkoZX25tDAGF5WcUoCVfS_jArNTysXNFxwpZIreBE2PcRawns1SeSc3M9jn3aMmmElsMjarhiCwHIKU8LPBhWBALQo2yw5WFTs0f_xS8JvcqFMHv2PgmTBtMBYW3QtM711YOg" 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/3d/7c/3d7c6845ae7a9de46b3f56764da2fc2c82edebb1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/molbev/msl079"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Page 7266 of Mathematical Reviews Vol. , Issue 98K [page]

<span title="">1998</span> <i title="American Mathematical Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_mathematical-reviews" style="color: black;">Mathematical Reviews </a> </i> &nbsp;
Vincent Berry and Olivier Gascuel, Inferring evolutionary trees with strong combinatorial evidence (111-123); Kenneth Rice and Tandy Warnow, Parsimony is hard to beat!  ...  Goli¢ and Luke O’Connor, A combinatorial pattern matching problem with applications to cryptography (473-478); C. Barry Jay, A fresh look at parametric polymorphism: covariant types (525-533).  ... 
<span class="external-identifiers"> </span>
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Recapitulating phylogenies using k-mers: from trees to networks

Guillaume Bernard, Mark A. Ragan, Cheong Xin Chan
<span title="2016-11-29">2016</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
A typical phylogenetic inference aims to capture and represent, in the form of a tree, the evolutionary history of a family of molecular sequences.  ...  Our findings suggest that the network captures not only key aspects k of microbial genome evolution as inferred from a tree, but also features that are not treelike.  ...  used for tree inference 22 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.10225.1">doi:10.12688/f1000research.10225.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28105314">pmid:28105314</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5224691/">pmcid:PMC5224691</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ptmte5yoebeu5cbfqh7rifrfh4">fatcat:ptmte5yoebeu5cbfqh7rifrfh4</a> </span>
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Index

<span title="">2000</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/elaf5sq7lfdxfdejhkqbtz6qoq" style="color: black;">Theoretical Computer Science</a> </i> &nbsp;
Gascuel, Inferring evolutionary trees with strong combinatorial evidence (2) 271}298 Bonsangue, M.M., F. Arbab, J.W. de Bakker, J.J.M.M. Rutten, A. Scutella`and G. ( 1 ) 1 49} 90 Hedman, E.J., J.N.  ...  Nishizeki, Algorithms for generalized vertex-rankings of partial k-trees (2) 407}427 MeH tayer, D.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0304-3975(00)00178-x">doi:10.1016/s0304-3975(00)00178-x</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fl3kcc6xtrbjtlzhouuacu7ciu">fatcat:fl3kcc6xtrbjtlzhouuacu7ciu</a> </span>
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