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% GENERATED FROM http://phylnet.univ-mlv.fr
% by : anonymous
% IP : ec2-54-198-143-210.compute-1.amazonaws.com
% at : Thu, 19 Oct 2017 18:16:37 +0000 UTC
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% Selection : Keyword(s) = FromNetwork
%
% Complete Journal Names and Abbreviations (but to use them you have to delete the { and } around the abbreviations,
% and before that you may want to research/replace "" by "\url{" and "" by "}", it
% will be made automatically in a next update of the Who's Who...):
@String{UM = {Unpublished manuscript}}
@String{springer = {Springer Verlag}}
@String{LNCS = {Lecture Notes in Computer Science}}
@String{CABIOS = {Comput. Appl. Biosci.}}
@String{ABIO = {Applied Bioinformatics}}
@String{AHB = {Annals of Human Biology}}
@String{AMB = {Algorithms for Molecular Biology}}
@String{ARG = {Annual Review of Genetics}}
@String{BMB = {Bulletin of Mathematical Biology}}
@String{BMCEB = {BMC Evolutionary Biology}}
@String{BMCB = {BMC Bioinformatics}}
@String{CC = {Computers and Chemistry}}
@String{G = {Genomics}}
@String{GEN = {Genetics}}
@String{BIO = {Bioinformatics}}
@String{EBIO = {Evolutionary Bioinformatics}}
@String{GR = {Genome Research}}
@String{INCOMP = {INFORMS Journal on Computing}}
@String{IJP = {International Journal for Parasitology}}
@String{IJBRA = {The International Journal of Bioinformatics Research and Applications}}
@String{JBCB = {Journal of Bioinformatics and Computational Biology}}
@String{JCB = {Journal of Computational Biology}}
@String{JMB = {Journal of Molecular Biology}}
@String{JOMB = {Journal of Mathematical Biology}}
@String{JME = {Journal of Molecular Evolution}}
@String{MBIO = {Mathematical Biosciences}}
@String{MBE = {Molecular Biology and Evolution}}
@String{MOLE = {Molecular Ecology}}
@String{MPE = {Molecular Phylogenetics and Evolution}}
@String{NAR = {Nucleic Acids Research}}
@String{NG = {Nature Genetics}}
@String{PLONE = {PLoS ONE}}
@String{PSE = {Plant Systematics and Evolution}}
@String{SB = {Systematic Biology}}
@String{TCBB = {IEEE/ACM Transactions in Computational Biology and Bioinformatics}}
@String{TCSB2 = {Transactions on Computational Systems Biology II}}
@String{TEE = {TRENDS in Ecology and Evolution}}
@String{TPP = {Theoretical Population Biology}}
@String{PNAS = {Proceedings of the National Academy of Sciences}}
@String{BIBE05 = {Proceedings of the Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05)}}
@String{PLGw01 = {EMBO Workshop on Current Challenges and Problems in Phylogenetics (Isaac Newton Institute for Mathematical Sciences)}}
@String{PSB03 = {Proceedings of the eigth Pacific Symposium on Biocomputing (PSB'03)}}
@String{PSB04 = {Proceedings of the ninth Pacific Symposium on Biocomputing (PSB'04)}}
@String{PSB05 = {Proceedings of the tenth Pacific Symposium on Biocomputing (PSB'05)}}
@String{RECOMB97 = {Proceedings of the first Annual International Conference on Research in Computational Molecular Biology (RECOMB'97)}}
@String{RECOMB98 = {Proceedings of the second Annual International Conference on Research in Computational Molecular Biology (RECOMB'98)}}
@String{RECOMB99 = {Proceedings of the third Annual International Conference on Research in Computational Molecular Biology (RECOMB'99)}}
@String{RECOMB00 = {Proceedings of the fourth Annual International Conference on Research in Computational Molecular Biology (RECOMB'00)}}
@String{RECOMB01 = {Proceedings of the fifth Annual International Conference on Research in Computational Molecular Biology (RECOMB'01)}}
@String{RECOMB02 = {Proceedings of the sixth Annual International Conference on Research in Computational Molecular Biology (RECOMB'02)}}
@String{RECOMB03 = {Proceedings of the seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'03)}}
@String{RECOMB04 = {Proceedings of the eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB'04)}}
@String{RECOMB05 = {Proceedings of the ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB'05)}}
@String{RECOMB06 = {Proceedings of the tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB'06)}}
@String{RECOMB07 = {Proceedings of the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07)}}
@String{RECOMB08 = {Proceedings of the twelfth Annual International Conference on Research in Computational Molecular Biology (RECOMB'08)}}
@String{RECOMB09 = {Proceedings of the 13$^{th}$ Annual International Conference on Research in Computational Molecular Biology (RECOMB'09)}}
@String{ISBRA05 = {Proceedings of the first International Symposium on Bioinformatics Research and Applications (ISBRA'05)}}
@String{ISBRA06 = {Proceedings of the second International Symposium on Bioinformatics Research and Applications (ISBRA'06)}}
@String{ISBRA07 = {Proceedings of the third International Symposium on Bioinformatics Research and Applications (ISBRA'07)}}
@String{ECCB01 = {Proceedings of the first European Conference on Computational Biology (ECCB'01)}}
@String{ECCB02 = {Proceedings of the second European Conference on Computational Biology (ECCB'02)}}
@String{ECCB03 = {Proceedings of the third European Conference on Computational Biology (ECCB'03)}}
@String{ECCB04 = {Proceedings of the fourth European Conference on Computational Biology (ECCB'04)}}
@String{ECCB05 = {Proceedings of the fifth European Conference on Computational Biology (ECCB'05)}}
@String{ECCB06 = {Proceedings of the sixth European Conference on Computational Biology (ECCB'06)}}
@String{ECCB07 = {Proceedings of the seventh European Conference on Computational Biology (ECCB'07)}}
@String{ECCB08 = {Proceedings of the eighth European Conference on Computational Biology (ECCB'08)}}
@String{APBC05 = {Proceedings of the Third Asia-Pacific Bioinformatics Conference (APBC'05)}}
@String{APBC06 = {Proceedings of the Fourth Asia-Pacific Bioinformatics Conference (APBC'06)}}
@String{APBC08 = {Proceedings of the Sixth Asia-Pacific Bioinformatics Conference (APBC'08)}}
@String{SAC01 = {Proceedings of the 16th ACM Symposium on Applied Computing (SAC'01)}}
@String{CSB03 = {Proceedings of the 2003 IEEE Computational Systems Bioinformatics Conference (CSB2003)}}
@String{CSB05 = {Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005)}}
@String{CSB06 = {Proceedings of the 2006 IEEE Computational Systems Bioinformatics Conference (CSB2006)}}
@String{WABI01 = {Proceedings of the first Workshop on Algorithms in Bioinformatics (WABI'01)}}
@String{WABI02 = {Proceedings of the second Workshop on Algorithms in Bioinformatics (WABI'02)}}
@String{WABI03 = {Proceedings of the third Workshop on Algorithms in Bioinformatics (WABI'03)}}
@String{WABI04 = {Proceedings of the fourth Workshop on Algorithms in Bioinformatics (WABI'04)}}
@String{WABI05 = {Proceedings of the fifth Workshop on Algorithms in Bioinformatics (WABI'05)}}
@String{WABI06 = {Proceedings of the sixth Workshop on Algorithms in Bioinformatics (WABI'06)}}
@String{WABI07 = {Proceedings of the seventh Workshop on Algorithms in Bioinformatics (WABI'07)}}
@String{WABI08 = {Proceedings of the eighth Workshop on Algorithms in Bioinformatics (WABI'08)}}
@String{ISMB05 = {Proceedings of the $13^{th}$ International Conference on Intelligent Systems in Molecular Biology (ISMB'05)}}
@String{ISMB11 = {Proceedings of the $19^{th}$ International Conference on Intelligent Systems in Molecular Biology (ISMB'05)}}
@String{ISAAC04 = {Proceedings of the $15^{th}$ International Symposium on Algorithms and Computation (ISAAC'04)}}
@String{ISAAC05 = {Proceedings of the $16^{th}$ International Symposium on Algorithms and Computation (ISAAC'05)}}
@String{MFCS05 = {Proceedings of the $30^{th}$ International Symposium on Mathematical Foundations of Computer Science (MFCS'05)}}
@String{MCCMB11 = {Proceedings of the fifth Moscow Conference on Computational Molecular Biology (MCCMB11'11)}}
@String{IWBRA05 = {Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA'05)}}
@String{IFCS00 = {Data Analysis, Classification, and Related Methods, Proceedings of the seventh Conference on the International Federation of Classification Societies (IFCS'00)}}
@String{IFCS02 = {Proceedings of the eighth Conference of the International Federation of Classification Societies (IFCS'02)}}
@String{IFCS04 = {Proceedings of the ninth Conference of the International Federation of Classification Societies (IFCS'04)}}
@String{CPM98 = {Proceedings of the ninth Annual Symposium on Combinatorial Pattern Matching (CPM'98)}}
@String{CPM07 = {Proceedings of the $18^{th}$ Annual Symposium on Combinatorial Pattern Matching (CPM'07)}}
@String{CPM07 = {Proceedings of the $18^{th}$ Annual Symposium on Combinatorial Pattern Matching (CPM'07)}}
@String{COCOON04 = {Proceedings of the tenth Annual International Computing and Combinatorics Conference (COCOON'04)}}
@String{COCOON05 = {Proceedings of the $11^{th}$ Annual International Computing and Combinatorics Conference (COCOON'06)}}
@String{COCOON06 = {Proceedings of the $12^{th}$ Annual International Computing and Combinatorics Conference (COCOON'06)}}
@String{COCOON07 = {Proceedings of the $13^{th}$ Annual International Computing and Combinatorics Conference (COCOON'07)}}
@String{COCOA07 = {Proceedings of the first International Conference on Combinatorial Optimization and Applications (COCOA'07)}}
@String{COCOA08 = {Proceedings of the second International Conference on Combinatorial Optimization and Applications (COCOA'08)}}
@String{PADL03 = {Proceedings of the fifth International Symposium on Practical Aspects of Declarative Languages (PADL'03)}}
@String{SODA94 = {Proceedings of the fifth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'94)}}
@String{SODA05 = {Proceedings of the $16^{th}$ Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'05)}}
@String{SEA10 = {Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10)}}
@String{ADM = {Annals of Discrete Mathematics}}
@String{ACOM = {Annals of Combinatorics}}
@String{ALG = {Algorithmica}}
@String{C = {Combinatorica}}
@String{CN = {Congressus Numerantium}}
@String{CSQ = {Computational Statistics Quarterly}}
@String{DCG = {Discrete and Computational Geometry}}
@String{DM = {Discrete Mathematics}}
@String{DAM = {Discrete Applied Mathematics}}
@String{EJC = {European Journal of Combinatorics}}
@String{IPL = {Information Processing Letters}}
@String{JADM = {SIAM Journal on Algebraic and Discrete Methods}}
@String{JCLA = {Journal of Classification}}
@String{JCO = {Journal of Combinatorial Optimization}}
@String{JDM = {SIAM Journal on Discrete Mathematics}}
@String{JAM = {SIAM Journal on Applied Mathematics}}
@String{JMAA = {SIAM Journal on Matrix Analysis and Applications}}
@String{JOC = {SIAM Journal on Computing}}
@String{JCTB = {Journal of Combinatorial Theory Series B}}
@String{JGT = {Journal of Graph Theory}}
@String{TCS = {Theoretical Computer Science}}
@String{JACM = {Journal of the ACM (JACM)}}
@String{JOA = {Journal of Algorithms}}
@String{DMTCS = {Discrete Mathematics and Theoretical Computer Science}}
@string{ICOMP = {Information and Computation}}
%
% 53 out of 61 publication(s) listed below is/are indexed by Scopus. Use the URL below to access it/them.
% 1) Go to http://www.scopus.com/search/form.url?display=advanced&clear=t&origin=SearchAffiliationLookup
% 2) Type the following text in the search box:
% DOI(http://dx.doi.org/10.1142/9789812770998_0011) OR DOI(http://dx.doi.org/10.1007/11428848_117) OR DOI(http://dx.doi.org/10.1007/11567752_6) OR DOI(http://dx.doi.org/10.1080/10635150590906046) OR DOI(http://dx.doi.org/10.1007/s00026-006-0280-z) OR DOI(http://dx.doi.org/10.1007/s11538-006-9187-4) OR DOI(http://dx.doi.org/10.1016/j.tcs.2008.04.019) OR DOI(http://dx.doi.org/10.1007/BFb0030789) OR DOI(http://dx.doi.org/10.1186/1471-2105-15-127) OR DOI(http://dx.doi.org/10.1155/2014/254279) OR DOI(http://dx.doi.org/10.1109/TCBB.2012.52) OR DOI(http://dx.doi.org/10.1007/s11538-010-9624-2) OR DOI(http://dx.doi.org/10.1016/j.ipl.2010.07.027) OR DOI(http://dx.doi.org/10.1016/j.tpb.2008.10.004) OR DOI(http://dx.doi.org/10.1093/bioinformatics/btr210) OR DOI(http://dx.doi.org/10.1093/sysbio/syp058) OR DOI(http://dx.doi.org/10.1109/TCBB.2008.54) OR DOI(http://dx.doi.org/10.1186/1748-7188-7-13) OR DOI(http://dx.doi.org/10.1089/cmb.2011.0254) OR DOI(http://dx.doi.org/10.1007/978-3-642-28839-5_15) OR DOI(http://dx.doi.org/10.1007/978-3-642-31265-6_31) OR DOI(http://gradworks.umi.com/35/11/3511361.html) OR DOI(http://arxiv.org/abs/1209.0871) OR DOI(http://arxiv.org/abs/1209.1040) OR DOI(http://dx.doi.org/10.1137/140959948) OR DOI(http://dx.doi.org/10.1137/12089394x) OR DOI(http://dx.doi.org/10.1093/sysbio/syt037) OR DOI(http://dx.doi.org/10.1142/S0219720012500254) OR DOI(http://dx.doi.org/10.1016/j.jda.2013.10.002) OR DOI(http://dx.doi.org/10.1111/cla.12062) OR DOI(http://dx.doi.org/10.1186/1471-2105-14-S15-S6) OR DOI(http://dx.doi.org/10.1089/cmb.2013.0134) OR DOI(http://dx.doi.org/10.1371/journal.pcbi.1003649) OR DOI(http://dx.doi.org/10.1109/ICCABS.2011.5729883 ) OR DOI(http://dx.doi.org/10.1093/sysbio/syu076) OR DOI(http://dx.doi.org/10.1007/s00285-015-0899-7) OR DOI(http://dx.doi.org/10.1007/978-3-319-16706-0_12) OR DOI(http://dx.doi.org/10.1109/JCSSE.2015.7219820) OR DOI(http://dx.doi.org/10.1007/978-3-319-31957-5) OR DOI(http://dx.doi.org/10.1007/978-3-319-29516-9_17) OR DOI(http://dx.doi.org/10.1016/j.aam.2016.04.004) OR DOI(http://dx.doi.org/10.1007/978-3-319-15612-5_7) OR DOI(http://dx.doi.org/10.1186/s12859-015-0721-y) OR DOI(http://dx.doi.org/10.1186/1471-2164-16-S10-S6) OR DOI(http://dx.doi.org/10.1101/023986) OR DOI(http://dx.doi.org/10.1007/s11538-016-0199-4) OR DOI(https://doi.org/10.1007/s00453-017-0366-5) OR DOI(http://dx.doi.org/10.1093/sysbio/syw097) OR DOI(http://dx.doi.org/10.1016/j.ic.2016.11.001) OR DOI(http://dx.doi.org/10.1186/s12864-017-3500-5) OR DOI(https://doi.org/10.1016/j.ipl.2017.03.002) OR DOI(https://doi.org/10.1016/j.jtbi.2017.01.024) OR DOI(http://dx.doi.org/10.1007/978-3-319-58163-7_8)
%
@InProceedings{KNTX2007,
AUTHOR = {Kanj, Iyad A. and Nakhleh, Luay and Than, Cuong and Xia, Ge},
TITLE = {Seeing the Trees and Their Branches in the Network is Hard},
YEAR = {2007},
BOOKTITLE = {Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS'07)},
URL = {http://dx.doi.org/10.1142/9789812770998_0011},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/ictcs07.pdf},
ANNOTE = {BIBUPDATE : },
KEYWORDS = {evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment}
}
@InProceedings{NakhlehWang2005a,
AUTHOR = {Nakhleh, Luay and Wang, Li-San},
TITLE = {Phylogenetic Networks, Trees, and Clusters},
YEAR = {2005},
BOOKTITLE = {IWBRA05},
VOLUME = {3515},
PAGES = {919-926},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11428848_117},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/NakhlehWang.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment}
}
@InProceedings{NakhlehWang2005b,
AUTHOR = {Nakhleh, Luay and Wang, Li-San},
TITLE = {Phylogenetic Networks: Properties and Relationship to Trees and Clusters},
YEAR = {2005},
BOOKTITLE = {TCSB2},
VOLUME = {3680},
PAGES = {82-99},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/11567752_6},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/LNCS_TCSB05.pdf},
ANNOTE = {BIBUPDATE : 20070917},
KEYWORDS = {cluster containment, evaluation, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree child network, tree containment}
}
@Article{WBLHM2005,
AUTHOR = {Winkworth, Richard C. and Bryant, David and Lockhart, Peter J. and Havell, David and Moulton, Vincent},
TITLE = {Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths},
YEAR = {2005},
JOURNAL = {Systematic Biology},
VOLUME = {54},
NUMBER = {1},
PAGES = {56-65},
URL = {http://dx.doi.org/10.1080/10635150590906046},
NOTE = {http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf},
ANNOTE = {CITE : },
KEYWORDS = {abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network}
}
@Article{Willson2006a,
AUTHOR = {Willson, Stephen J.},
TITLE = {Unique solvability of certain hybrid networks from their distances},
YEAR = {2006},
JOURNAL = {ACOM},
VOLUME = {10},
NUMBER = {1},
PAGES = {165-178},
URL = {http://dx.doi.org/10.1007/s00026-006-0280-z},
NOTE = {http://www.public.iastate.edu/~swillson/Solvability.pdf},
ANNOTE = {BIBUPDATE : 20070924},
KEYWORDS = {from distances, from network, labeling, phylogenetic network, phylogeny}
}
@Article{Willson2007a,
AUTHOR = {Willson, Stephen J.},
TITLE = {Unique determination of some homoplasies at hybridization events},
YEAR = {2007},
JOURNAL = {BMB},
VOLUME = {69},
NUMBER = {5},
PAGES = {1709-1725},
URL = {http://dx.doi.org/10.1007/s11538-006-9187-4},
NOTE = {http://www.public.iastate.edu/~swillson/unique.det.pdf},
ANNOTE = {BIBUPDATE : 20071216},
KEYWORDS = {explicit network, from network, hybridization, labeling, normal network, phylogenetic network, tree child network}
}
@Article{KNTX2008,
AUTHOR = {Kanj, Iyad A. and Nakhleh, Luay and Than, Cuong and Xia, Ge},
TITLE = {Seeing the Trees and Their Branches in the Network is Hard},
YEAR = {2008},
JOURNAL = {TCS},
VOLUME = {401},
PAGES = {153-164},
URL = {http://dx.doi.org/10.1016/j.tcs.2008.04.019},
NOTE = {http://www.cs.rice.edu/~nakhleh/Papers/tcs08.pdf},
ANNOTE = {BIBUPDATE : },
KEYWORDS = {evaluation, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, tree containment}
}
@InProceedings{MWL1998,
AUTHOR = {Ma, Bin and Wang, Lusheng and Li, Ming},
TITLE = {Fixed topology alignment with recombination},
YEAR = {1998},
BOOKTITLE = {CPM98},
VOLUME = {1448},
PAGES = {174-188},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/BFb0030789},
NOTE = {http://dx.doi.org/10.1007/BFb0030789},
ANNOTE = {BIBUPDATE : 20081225},
KEYWORDS = {approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination}
}
@Article{MWL2000,
AUTHOR = {Ma, Bin and Wang, Lusheng and Li, Ming},
TITLE = {Fixed topology alignment with recombination},
YEAR = {2000},
JOURNAL = {DAM},
VOLUME = {104},
PAGES = {281-300},
URL = {http://dx.doi.org/10.1186/1471-2105-15-127},
NOTE = {http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759},
ANNOTE = {BIBUPDATE : 20081225},
KEYWORDS = {approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination}
}
@Article{CLRV2014,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc and Valiente, Gabriel},
TITLE = {The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete},
YEAR = {2014},
JOURNAL = {The Scientific World Journal},
VOLUME = {2014},
NUMBER = {254279},
PAGES = {1-6},
URL = {http://dx.doi.org/10.1155/2014/254279},
NOTE = {http://arxiv.org/abs/0902.4640},
KEYWORDS = {abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network}
}
@Article{Willson2012,
AUTHOR = {Willson, Stephen J.},
TITLE = {CSD Homomorphisms Between Phylogenetic Networks},
YEAR = {2012},
JOURNAL = {TCBB},
VOLUME = {9},
NUMBER = {4},
URL = {http://dx.doi.org/10.1109/TCBB.2012.52},
NOTE = {http://www.public.iastate.edu/~swillson/Relationships11IEEE.pdf, preliminary version entitled *Relationships Among Phylogenetic Networks*},
KEYWORDS = {explicit network, from network, from quartets, phylogenetic network}
}
@Article{Willson2011,
AUTHOR = {Willson, Stephen J.},
TITLE = {Restricted trees: simplifying networks with bottlenecks},
YEAR = {2011},
JOURNAL = {BMB},
VOLUME = {73},
NUMBER = {10},
PAGES = {2322-2338},
URL = {http://dx.doi.org/10.1007/s11538-010-9624-2},
NOTE = {http://arxiv.org/abs/1005.4956},
KEYWORDS = {from network, phylogenetic network}
}
@Article{ISS2010b,
AUTHOR = {van Iersel, Leo and Semple, Charles and Steel, Mike},
TITLE = {Locating a tree in a phylogenetic network},
YEAR = {2010},
JOURNAL = {IPL},
VOLUME = {110},
NUMBER = {23},
URL = {http://dx.doi.org/10.1016/j.ipl.2010.07.027},
NOTE = {http://arxiv.org/abs/1006.3122},
KEYWORDS = {cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree child network, tree containment, tree sibling network}
}
@Article{MengKubatko2009,
AUTHOR = {Meng, Chen and Kubatko, Laura S.},
TITLE = {Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model},
YEAR = {2009},
JOURNAL = {Theoretical Population Biology},
VOLUME = {75},
NUMBER = {1},
PAGES = {35-45},
URL = {http://dx.doi.org/10.1016/j.tpb.2008.10.004},
NOTE = {http://dx.doi.org/10.1016/j.tpb.2008.10.004},
KEYWORDS = {bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model}
}
@Misc{CMF2010,
AUTHOR = {Cardona, Gabriel and Llabr{\~A}İs, Merc{\~A}¨ and Rossell{\~A}³, Francesc},
TITLE = {A metric for galled networks},
YEAR = {2010},
NOTE = {http://arxiv4.library.cornell.edu/abs/1009.0652},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny}
}
@InProceedings{ScornavaccaHuson2011,
AUTHOR = {Scornavacca, Celine and Zickmann, Franziska and Huson, Daniel H.},
TITLE = {Tanglegrams for Rooted Phylogenetic Trees and Networks},
YEAR = {2011},
BOOKTITLE = {ISMB11},
VOLUME = {27},
NUMBER = {13},
PAGES = {i248-i256},
SERIES = {BIO},
URL = {http://dx.doi.org/10.1093/bioinformatics/btr210},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btr210},
KEYWORDS = {from network, heuristic, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization}
}
@Misc{ZDS2011,
AUTHOR = {Zhu, Sha and Degnan, James H. and Steel, Mike},
TITLE = {Probabilistic modeling of gene trees given species networks},
YEAR = {2011},
NOTE = {Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf},
KEYWORDS = {from network, generation, phylogenetic network, phylogeny, statistical model}
}
@Article{MKH2009,
AUTHOR = {Minh, Bui Quang and Klaere, Steffen and von Haeseler, Arndt},
TITLE = {Taxon Selection under Split Diversity},
YEAR = {2009},
JOURNAL = {Systematic Biology},
VOLUME = {58},
NUMBER = {6},
PAGES = {586-594},
URL = {http://dx.doi.org/10.1093/sysbio/syp058},
NOTE = {http://dx.doi.org/10.1093/sysbio/syp058},
KEYWORDS = {abstract network, circular split system, diversity, from network, phylogenetic network, split network}
}
@Article{MPKH2009,
AUTHOR = {Minh, Bui Quang and Pardi, Fabio and Klaere, Steffen and von Haeseler, Arndt},
TITLE = {Budgeted Phylogenetic Diversity on Circular Split Systems},
YEAR = {2009},
JOURNAL = {TCBB},
VOLUME = {6},
NUMBER = {1},
PAGES = {22-29},
URL = {http://dx.doi.org/10.1109/TCBB.2008.54},
NOTE = {http://dx.doi.org/10.1109/TCBB.2008.54},
KEYWORDS = {abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network}
}
@Article{Willson2012b,
AUTHOR = {Willson, Stephen J.},
TITLE = {Tree-average distances on certain phylogenetic networks have their weights uniquely determined},
YEAR = {2012},
JOURNAL = {ALMOB},
VOLUME = {7},
NUMBER = {13},
URL = {http://dx.doi.org/10.1186/1748-7188-7-13},
NOTE = {hhttp://www.public.iastate.edu/~swillson/Tree-AverageDis10All.pdf},
KEYWORDS = {from distances, from network, normal network, phylogenetic network, phylogeny, reconstruction, tree child network}
}
@Article{KRFJZK2012,
AUTHOR = {Kirkpatrick, Bonnie and Reshef, Yakir and Finucane, Hilary and Jiang, Haitao and Zhu, Binhai and Karp, Richard M.},
TITLE = {Comparing Pedigree Graphs},
YEAR = {2012},
JOURNAL = {JCB},
VOLUME = {19},
NUMBER = {9},
PAGES = {998-1014},
URL = {http://dx.doi.org/10.1089/cmb.2011.0254},
NOTE = {http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010},
KEYWORDS = {distance between networks, from network, pedigree}
}
@InProceedings{ACSP2012,
AUTHOR = {Alves, Marco and Alves, Jo{\~A}£d and Camacho, Rui and Soares, Pedro and Pereira, Lu{\~A}sa},
TITLE = {From Networks to Trees},
YEAR = {2012},
BOOKTITLE = {PACBB'12},
VOLUME = {154},
PAGES = {129-136},
SERIES = {Advances in Intelligent and Soft Computing},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-28839-5_15},
KEYWORDS = {from network, phylogenetic network, phylogeny}
}
@InProceedings{JanssonLingas2012,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2012},
BOOKTITLE = {CPM12},
VOLUME = {7354},
PAGES = {385-398},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-642-31265-6_31},
NOTE = {http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf},
KEYWORDS = {distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance}
}
@PhdThesis{Birckner2012,
AUTHOR = {Bickner, Devin Robert},
TITLE = {On normal networks},
YEAR = {2012},
SCHOOL = {Iowa State University, U.S.A.},
URL = {http://gradworks.umi.com/35/11/3511361.html},
NOTE = {http://gradworks.umi.com/3511361.pdf},
KEYWORDS = {distance between networks, explicit network, from network, from trees, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, SPR distance}
}
@Misc{AlcalaRossello2012,
AUTHOR = {Alcal{\~A} Mena, Adri{\~A} and Rossell{\~A}³, Francesc},
TITLE = {Ternary graph isomorphism in polynomial time, after Luks},
YEAR = {2012},
URL = {http://arxiv.org/abs/1209.0871},
NOTE = {http://arxiv.org/abs/1209.0871},
KEYWORDS = {distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE}
}
@MastersThesis{Alcala2012,
AUTHOR = {Alcal{\~A} Mena, Adri{\~A} },
TITLE = {Trivalent Graph isomorphism in polynomial time},
YEAR = {2012},
SCHOOL = {Universidad de Cantabria, Spain},
URL = {http://arxiv.org/abs/1209.1040},
NOTE = {http://arxiv.org/abs/1209.1040},
KEYWORDS = {distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE}
}
@Article{FIKS2015,
AUTHOR = {Fischer, Mareike and van Iersel, Leo and Kelk, Steven and Scornavacca, Celine},
TITLE = {On Computing The Maximum Parsimony Score Of A Phylogenetic Network},
YEAR = {2015},
JOURNAL = {SIDMA},
VOLUME = {29},
NUMBER = {1},
PAGES = {559-585},
URL = {http://dx.doi.org/10.1137/140959948},
NOTE = {http://arxiv.org/abs/1302.2430},
KEYWORDS = {APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software}
}
@Misc{ZDE2013,
AUTHOR = {Zhu, Sha and Degnan, James H. and Eldon, Bjarki},
TITLE = {Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees},
YEAR = {2013},
NOTE = {http://arxiv.org/abs/1303.0673},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software}
}
@Article{LSS2013,
AUTHOR = {Linz, Simone and St. John, Katherine and Semple, Charles},
TITLE = {Counting trees in a phylogenetic network is #P-complete},
YEAR = {2013},
JOURNAL = {SICOMP},
VOLUME = {42},
NUMBER = {4},
PAGES = {1768-1776},
URL = {http://dx.doi.org/10.1137/12089394x},
NOTE = {http://ab.inf.uni-tuebingen.de/people/linz/publications/counting.pdf},
KEYWORDS = {counting, from network, phylogenetic network, phylogeny}
}
@Article{YBN2013,
AUTHOR = {Yu, Yun and Barnett, R. Matthew and Nakhleh, Luay},
TITLE = {Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting},
YEAR = {2013},
JOURNAL = {Systematic Biology},
VOLUME = {62},
NUMBER = {5},
PAGES = {738-751},
URL = {http://dx.doi.org/10.1093/sysbio/syt037},
KEYWORDS = {from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}
@PhdThesis{Zhu2013,
AUTHOR = {Zhu, Sha},
TITLE = {Stochastic tree models and probabilistic modelling of gene trees of given species networks},
YEAR = {2013},
SCHOOL = {University of Canterbury, New Zealand},
NOTE = {http://hdl.handle.net/10092/7944},
KEYWORDS = {from network, generation, phylogenetic network, phylogeny, simulation, statistical model}
}
@Article{SPBR2013,
AUTHOR = {Scornavacca, Celine and Wojciech, Paprotny and Berry, Vincent and Ranwez, Vincent},
TITLE = {Representing a set of reconciliations in a compact way},
YEAR = {2013},
JOURNAL = {JBCB},
VOLUME = {11},
NUMBER = {2},
PAGES = {1250025},
URL = {http://dx.doi.org/10.1142/S0219720012500254},
NOTE = {http://hal-lirmm.ccsd.cnrs.fr/lirmm-00818801},
KEYWORDS = {duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization}
}
@Misc{KLM2013,
AUTHOR = {Kelk, Steven and Linz, Simone and Morrison, David A.},
TITLE = {Fighting network space: it is time for an SQL-type language to filter phylogenetic networks},
YEAR = {2013},
NOTE = {http://arxiv.org/abs/1310.6844},
KEYWORDS = {database, explicit network, from network, phylogenetic network, phylogeny}
}
@Article{JanssonLingas2014,
AUTHOR = {Jansson, Jesper and Lingas, Andrzej},
TITLE = {Computing the rooted triplet distance between galled trees by counting triangles},
YEAR = {2014},
JOURNAL = {Journal of Discrete Algorithms},
VOLUME = {25},
PAGES = {66-78},
URL = {http://dx.doi.org/10.1016/j.jda.2013.10.002},
KEYWORDS = {distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance}
}
@Article{Wheeler2014,
AUTHOR = {Wheeler, Ward C},
TITLE = {Phyletic groups on networks},
YEAR = {2014},
JOURNAL = {Cladistics},
VOLUME = {30},
NUMBER = {4},
PAGES = {447-451},
URL = {http://dx.doi.org/10.1111/cla.12062},
NOTE = {http://dx.doi.org/10.1111/cla.12062},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny}
}
@InProceedings{YRN2013,
AUTHOR = {Yu, Yun and Ristic, Nikola and Nakhleh, Luay},
TITLE = {Fast algorithms and heuristics for phylogenomics under ILS and hybridization},
YEAR = {2013},
BOOKTITLE = {RECOMB-CG'13},
VOLUME = {14},
NUMBER = {Suppl 15},
PAGES = {S6},
SERIES = {BMCB},
URL = {http://dx.doi.org/10.1186/1471-2105-14-S15-S6},
KEYWORDS = {from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction}
}
@Article{KannanWheeler2014,
AUTHOR = {Kannan, Lavanya and Wheeler, Ward C},
TITLE = {Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming},
YEAR = {2014},
JOURNAL = {JCB},
VOLUME = {21},
NUMBER = {4},
PAGES = {303-319},
URL = {http://dx.doi.org/10.1089/cmb.2013.0134},
KEYWORDS = {explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction}
}
@Article{LDTSKN2014,
AUTHOR = {Liu, Kevin J. and Dai, Jingxuan and Truong, Kathy and Song, Ying and Kohn, Michael H. and Nakhleh, Luay},
TITLE = {An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes},
YEAR = {2014},
JOURNAL = {PLoS ONE},
VOLUME = {10},
NUMBER = {6},
PAGES = {e1003649},
URL = {http://dx.doi.org/10.1371/journal.pcbi.1003649},
NOTE = {http://arxiv.org/abs/1310.7989},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM}
}
@InProceedings{ZNWZ2011,
AUTHOR = {Zhang, Louxin and Ng, Yen Kaow and Wu, Taoyang and Zheng, Yu},
TITLE = {Network model and efficient method for detecting relative duplications or horizontal gene transfers},
YEAR = {2011},
BOOKTITLE = {ICCABS11},
PAGES = {214-219},
URL = {http://dx.doi.org/10.1109/ICCABS.2011.5729883 },
KEYWORDS = {dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction}
}
@Article{HIMW2015,
AUTHOR = {Huber, Katharina and van Iersel, Leo and Moulton, Vincent and Wu, Taoyang},
TITLE = {How much information is needed to infer reticulate evolutionary histories?},
YEAR = {2015},
JOURNAL = {Systematic Biology},
VOLUME = {64},
NUMBER = {1},
PAGES = {102-111},
URL = {http://dx.doi.org/10.1093/sysbio/syu076},
NOTE = {http://dx.doi.org/10.1093/sysbio/syu076},
KEYWORDS = {explicit network, from network, from rooted trees, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness}
}
@Article{HLMW2016,
AUTHOR = {Huber, Katharina and Linz, Simone and Moulton, Vincent and Wu, Taoyang},
TITLE = {Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations},
YEAR = {2016},
JOURNAL = {JOMB},
VOLUME = {72},
NUMBER = {2},
PAGES = {699-725},
URL = {http://dx.doi.org/10.1007/s00285-015-0899-7},
KEYWORDS = {bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny}
}
@InProceedings{GGLVZ2015,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}İphane and Zhang, Louxin},
TITLE = {Locating a Tree in A Phylogenetic Network in Quadratic Time},
YEAR = {2015},
BOOKTITLE = {RECOMB15},
VOLUME = {9029},
PAGES = {96-107},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-16706-0_12},
NOTE = {https://hal.archives-ouvertes.fr/hal-01116231/en},
KEYWORDS = {evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}
@InProceedings{FKP2015,
AUTHOR = {Fakcharoenphol, Jittat and Kumpijit, Tanee and Putwattana, Attakorn},
TITLE = {A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks},
YEAR = {2015},
BOOKTITLE = {Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15)},
PAGES = {337-342},
PUBLISHER = {IEEE},
URL = {http://dx.doi.org/10.1109/JCSSE.2015.7219820},
KEYWORDS = {dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}
@InProceedings{GDZ2016,
AUTHOR = {Gunawan, Andreas and DasGupta, Bhaskar and Zhang, Louxin},
TITLE = {Locating a Tree in a Reticulation-Visible Network in Cubic Time},
YEAR = {2016},
BOOKTITLE = {RECOMB2016},
VOLUME = {9649},
PAGES = {266},
SERIES = {LNBI},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-31957-5},
NOTE = {http://arxiv.org/abs/1507.02119},
KEYWORDS = {cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment}
}
@InProceedings{GGLVZ2016,
AUTHOR = {Gambette, Philippe and Gunawan, Andreas and Labarre, Anthony and Vialette, St{\~A}İphane and Zhang, Louxin},
TITLE = {Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time},
YEAR = {2016},
BOOKTITLE = {IWOCA15},
VOLUME = {9538},
PAGES = {197-208},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-29516-9_17},
NOTE = {https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 },
KEYWORDS = {explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment}
}
@Article{BordewichSemple2016b,
AUTHOR = {Bordewich, Magnus and Semple, Charles},
TITLE = {Reticulation-visible networks},
YEAR = {2016},
JOURNAL = {Advances in Applied Mathematics},
VOLUME = {78},
PAGES = {114-141},
URL = {http://dx.doi.org/10.1016/j.aam.2016.04.004},
NOTE = {http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment}
}
@InProceedings{FischerPeters2015,
AUTHOR = {Fischer, Johannes and Peters, Daniel},
TITLE = {A Practical Succinct Data Structure for Tree-Like Graphs},
YEAR = {2015},
BOOKTITLE = {WALCOM15},
VOLUME = {8973},
PAGES = {65-76},
SERIES = {LNCS},
PUBLISHER = {springer},
URL = {http://dx.doi.org/10.1007/978-3-319-15612-5_7},
KEYWORDS = {compression, from network, phylogenetic network, phylogeny}
}
@Article{ZDGE2015,
AUTHOR = {Zhu, Sha and Degnan, James H. and Goldstein, Sharyn J. and Eldon, Bjarki},
TITLE = {Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees},
YEAR = {2015},
JOURNAL = {BMCB},
VOLUME = {16},
NUMBER = {292},
PAGES = {1-7},
URL = {http://dx.doi.org/10.1186/s12859-015-0721-y},
NOTE = {http://dx.doi.org/10.1186/s12859-015-0721-y},
KEYWORDS = {explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software}
}
@InProceedings{ToScornavacca2015,
AUTHOR = {To, Thu-Hien and Scornavacca, Celine},
TITLE = {Efficient algorithms for reconciling gene trees and species networks via duplication and loss events},
YEAR = {2015},
BOOKTITLE = {RECOMB-CG15},
VOLUME = {16(Suppl 10)},
NUMBER = {S6},
PAGES = {1-14},
SERIES = {BMC Genomics},
PUBLISHER = {BioMed Central},
URL = {http://dx.doi.org/10.1186/1471-2164-16-S10-S6},
NOTE = {http://dx.doi.org/10.1186/1471-2164-16-S10-S6},
KEYWORDS = {explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction}
}
@Misc{JhwuengOMeara2015,
AUTHOR = {Jhwueng, Dwueng-Chwuan and O'Meara, Brian},
TITLE = {Trait Evolution on Phylogenetic Networks},
YEAR = {2015},
URL = {http://dx.doi.org/10.1101/023986},
NOTE = {http://dx.doi.org/10.1101/023986},
KEYWORDS = {explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model}
}
@Article{GIKPS2016,
AUTHOR = {Gambette, Philippe and van Iersel, Leo and Kelk, Steven and Pardi, Fabio and Scornavacca, Celine},
TITLE = {Do branch lengths help to locate a tree in a phylogenetic network?},
YEAR = {2016},
JOURNAL = {BMB},
VOLUME = {78},
NUMBER = {9},
PAGES = {1773-1795},
URL = {http://dx.doi.org/10.1007/s11538-016-0199-4},
NOTE = {http://arxiv.org/abs/1607.06285},
KEYWORDS = {branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network}
}
@InProceedings{GLZ2016,
AUTHOR = {Gunawan, Andreas and Lu, Bingxin and Zhang, Louxin},
TITLE = {A program for verification of phylogenetic network models},
YEAR = {2016},
BOOKTITLE = {ECCB16},
VOLUME = {32},
NUMBER = {17},
PAGES = {i503-i510},
SERIES = {BIO},
NOTE = {http://dx.doi.org/10.1093/bioinformatics/btw467},
KEYWORDS = {exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment}
}
@Article{IKSSB2017,
AUTHOR = {van Iersel, Leo and Kelk, Steven and Stamoulis, Giorgios and Stougie, Leen and Boes, Olivier},
TITLE = {On unrooted and root-uncertain variants of several well-known phylogenetic network problems},
YEAR = {2017},
JOURNAL = {ALG},
URL = {https://doi.org/10.1007/s00453-017-0366-5},
NOTE = {https://hal.inria.fr/hal-01599716, to appear},
KEYWORDS = {explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment}
}
@Article{ShaDegnan2017,
AUTHOR = {Zhu, Sha and Degnan, James H.},
TITLE = {Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent},
YEAR = {2017},
JOURNAL = {SB},
VOLUME = {66},
NUMBER = {2},
PAGES = {283-298},
URL = {http://dx.doi.org/10.1093/sysbio/syw097},
NOTE = {presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g},
KEYWORDS = {branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness}
}
@Article{GDZ2017,
AUTHOR = {Gunawan, Andreas and DasGupta, Bhaskar and Zhang, Louxin},
TITLE = {A decomposition theorem and two algorithms for reticulation-visible networks},
YEAR = {2017},
JOURNAL = {Information and Computation},
VOLUME = {252},
PAGES = {161-175},
URL = {http://dx.doi.org/10.1016/j.ic.2016.11.001},
NOTE = {https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf},
KEYWORDS = {cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.}
}
@Misc{Weller2017,
AUTHOR = {Weller, Mathias},
TITLE = {Linear-Time Tree Containment in Phylogenetic Networks},
YEAR = {2017},
NOTE = {https://arxiv.org/abs/1702.06364},
KEYWORDS = {explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment}
}
@Misc{FHMW2017,
AUTHOR = {Francis, Andrew R. and Huber, Katharina and Moulton, Vincent and Wu, Taoyang},
TITLE = {Bounds for phylogenetic network space metrics},
YEAR = {2017},
NOTE = {https://arxiv.org/abs/1702.05609},
KEYWORDS = {bound, distance between networks, from network, NNI distance, SPR distance, TBR distance}
}
@InProceedings{LZL2017,
AUTHOR = {Lu, Bingxin and Zhang, Louxin and Leong, Hon Wai},
TITLE = {A program to compute the soft Robinson-Foulds distance between phylogenetic networks},
YEAR = {2017},
BOOKTITLE = {APBC17},
VOLUME = {18},
NUMBER = {Suppl. 2},
PAGES = {111},
SERIES = {BMC Genomics},
URL = {http://dx.doi.org/10.1186/s12864-017-3500-5},
NOTE = {http://dx.doi.org/10.1186/s12864-017-3500-5},
KEYWORDS = {cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork}
}
@Article{MOW2017,
AUTHOR = {Moulton, Vincent and Oldman, James and Wu, Taoyang},
TITLE = {A cubic-time algorithm for computing the trinet distance between level-1 networks},
YEAR = {2017},
JOURNAL = {IPL},
VOLUME = {123},
PAGES = {36-41},
URL = {https://doi.org/10.1016/j.ipl.2017.03.002},
NOTE = {https://doi.org/10.1016/j.ipl.2017.03.002},
KEYWORDS = {distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet}
}
@Article{SPC2017,
AUTHOR = {Scornavacca, Celine and Pons, Joan Carles and Cardona, Gabriel},
TITLE = {Fast algorithm for the reconciliation of gene trees and LGT networks},
YEAR = {2017},
JOURNAL = {JTB},
VOLUME = {418},
PAGES = {129-137},
URL = {https://doi.org/10.1016/j.jtbi.2017.01.024},
KEYWORDS = {duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction}
}
@InProceedings{JRS2017,
AUTHOR = {Jansson, Jesper and Rajaby, Ramesh and Sung, Wing-Kin},
TITLE = {An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees},
YEAR = {2017},
BOOKTITLE = {AlCoB17},
VOLUME = {10252},
PAGES = {115-126},
SERIES = {LNCS},
PUBLISHER = {Springer},
URL = {http://dx.doi.org/10.1007/978-3-319-58163-7_8},
NOTE = {},
KEYWORDS = {distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance}
}