













Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:2227 of LNCS, Springer, 2020. Keywords: cluster containment, galled network, galled tree, nearlystable network, phylogenetic network, phylogeny, polynomial, reticulationvisible network, survey, time consistent network, tree containment, treebased network, treechild network.











Remie Janssen,
Mark Jones and
Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences. In AlCoB20, Vol. 12099:7792 of LNCS, Springer, 2020. Keywords: cherrypicking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, treechild network.





Remie Janssen and
Yukihiro Murakami. Linear Time Algorithm for TreeChild Network Containment. In AlCoB20, Vol. 12099:93107 of LNCS, Springer, 2020. Keywords: explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, treechild network, treechild sequence. Note: https://doi.org/10.1007/9783030422660_8.



Leo van Iersel,
Remie Janssen,
Mark Jones,
Yukihiro Murakami and
Norbert Zeh. PolynomialTime Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation. In TCBB, Vol. 17(1):1426, 2020. Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, reconstruction. Note: http://pure.tudelft.nl/ws/portalfiles/portal/71270795/08798653.pdf.
















Joan Carles Pons,
Charles Semple and
Mike Steel. Treebased networks: characterisations, metrics, and support trees. In JOMB, Vol. 78(4):899918, 2019. Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, treebased network. Note: https://arxiv.org/abs/1710.07836.









Janosch Döcker,
Leo van Iersel,
Steven Kelk and
Simone Linz. Deciding the existence of a cherrypicking sequence is hard on two trees. In DAM, Vol. 260:131143, 2019. Keywords: cherrypicking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporalhybridization number, time consistent network, treechild network. Note: https://arxiv.org/abs/1712.02965.







Andreas Gunawan,
Hongwei Yan and
Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019. Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasireticulationvisible network, reticulationvisible network, tree containment, treechild network. Note: https://arxiv.org/abs/1806.07625.



R. A. Leo Elworth,
Huw A. Ogilvie,
Jiafan Zhu and
Luay Nakhleh. Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. In
Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29 of Computational Biology, Springer, 2019. Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey. Note: https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf



Louxin Zhang. Clusters, Trees, and Phylogenetic Network Classes. In
Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29:277315 of Computational Biology, Springer, 2019. Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment.





Juan Wang and
Maozu Guo. IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs. In ICNCFSKD19, Vol. 1075:894900 of Advances in Intelligent Systems and Computing, Springer, 2019. Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program IGNet, Program LNetwork, reconstruction, software.



Yukihiro Murakami,
Leo van Iersel,
Remie Janssen,
Mark Jones and
Vincent Moulton. Reconstructing TreeChild Networks from ReticulateEdgeDeleted Subnetworks. In BMB, Vol. 81:38233863, 2019. Keywords: from subnetworks, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, treechild network, uniqueness. Note: https://doi.org/10.1007/s1153801900641w.





Juan Wang and
Maozu Guo. A review of metrics measuring dissimilarity for rooted phylogenetic networks. In Briefings in Bioinformatics, Vol. 20(6):19721980, 2019. Keywords: distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, treechild network.









Jesper Jansson,
Konstantinos Mampentzidis,
Ramesh Rajaby and
WingKin Sung. Computing the Rooted Triplet Distance Between Phylogenetic Networks. In IWOCA19, Vol. 11638:290303 of LNCS, Springer, 2019. Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, triplet distance.










Leo van Iersel,
Steven Kelk,
Giorgios Stamoulis,
Leen Stougie and
Olivier Boes. On unrooted and rootuncertain variants of several wellknown phylogenetic network problems. In ALG, Vol. 80(11):29933022, 2018. Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment. Note: https://hal.inria.fr/hal01599716.







Mathias Weller. LinearTime Tree Containment in Phylogenetic Networks. In RECOMBCG18, Vol. 11183:309323 of LNCS, Springer, 2018. Keywords: explicit network, from network, from rooted trees, nearlystable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulationvisible network, tree containment. Note: https://arxiv.org/abs/1702.06364.



Andrew R. Francis,
Katharina Huber,
Vincent Moulton and
Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):12291248, 2018. Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance. Note: https://arxiv.org/abs/1702.05609.



Hussein A. Hejase,
Natalie VandePol,
Gregory A. Bonito and
Kevin J. Liu. Fast and accurate statistical inference of phylogenetic networks using largescale genomic sequence data. In RECOMBCG18, Vol. 11183:242259 of LNCS, Springer, 2018. Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction. Note: http://biorxiv.org/content/early/2017/05/01/132795.



Andrew R. Francis,
Katharina Huber and
Vincent Moulton. Treebased unrooted phylogenetic networks. In BMB, Vol. 80(2):404416, 2018. Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, treebased network, Unrooted treebased network. Note: https://arxiv.org/abs/1704.02062.



Magnus Bordewich,
Charles Semple and
Nihan Tokac. Constructing treechild networks from distance matrices. In Algorithmica, Vol. 80(8):22402259, 2018. Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, treechild network, uniqueness. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.



Andreas Gunawan. Solving the Tree Containment Problem for Reticulationvisible Networks in Linear Time. In AlCoB18, Vol. 10849:2436 of LNCS, Springer, 2018. Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: https://arxiv.org/abs/1702.04088.



Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:6279, 2018. Keywords: explicit network, from network, from rooted trees, nearlystable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://halupecupem.archivesouvertes.fr/hal01575001/en/.



Remie Janssen,
Mark Jones,
Péter L. Erdös,
Leo van Iersel and
Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):21772208, 2018. Keywords: distance between networks, explicit network, from network, NNI moves, phylogenetic network, phylogeny, SPR distance. Note: https://arxiv.org/abs/1708.07656.





Sarah Bastkowski,
Daniel Mapleson,
Andreas Spillner,
Taoyang Wu,
Monika Balvociute and
Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):10571058, 2018. Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network. Note: https://doi.org/10.1101/169177.



Sebastien Roch and
KunChieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167176 of LNCS, Springer, 2018. Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network. Note: https://arxiv.org/abs/1707.05722.



Katharina Huber,
Vincent Moulton,
Charles Semple and
Taoyang Wu. Quarnet inference rules for level1 networks. In BMB, Vol. 80:21372153, 2018. Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: https://arxiv.org/abs/1711.06720.









Janosch Döcker and
Simone Linz. On the existence of a cherrypicking sequence. In TCS, Vol. 714:3650, 2018. Keywords: cherrypicking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporalhybridization number, time consistent network, treechild network. Note: https://arxiv.org/abs/1712.04127.





Leo van Iersel,
Mark Jones and
Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518542, 2018. Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction. Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.





Magnus Bordewich,
Katharina Huber,
Vincent Moulton and
Charles Semple. Recovering normal networks from shortest intertaxa distance information. In JOMB, Vol. 77(3):571594, 2018. Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.







Chi Zhang,
Huw A. Ogilvie,
Alexei J. Drummond and
Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504517, 2018. Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model. Note: https://dx.doi.org/10.1093/molbev/msx307.



Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018. Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness. Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.









Dingqiao Wen,
Yun Yu,
Jiafan Zhu and
Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735740, 2018. Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.



Jiafan Zhu,
Dingqiao Wen,
Yun Yu,
Heidi M. Meudt and
Luay Nakhleh. Bayesian inference of phylogenetic networks from biallelic genetic markers. In PLoS Computational Biology, Vol. 14(1):e1005932.132, 2018. Keywords: bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet. Note: https://doi.org/10.1371/journal.pcbi.1005932.





Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018. Keywords: cluster containment, explicit network, galled network, genetically stable network, nearlystable network, phylogenetic network, phylogeny, reticulationvisible network, tree containment. Note: https://scholarbank.nus.edu.sg/handle/10635/144270.



Leo van Iersel,
Remie Janssen,
Mark Jones,
Yukihiro Murakami and
Norbert Zeh. PolynomialTime Algorithms for Phylogenetic Inference Problems. In AlCoB18, Vol. 10849:3749 of LNCS, Springer, 2018. Keywords: hybridization, minimum number, parental hybridization, phylogenetic network, phylogeny, polynomial, reconstruction. Note: https://research.tudelft.nl/files/53686721/10.1007_978_3_319_91938_6_4.pdf.






Katharina Huber,
Leo van Iersel,
Vincent Moulton,
Celine Scornavacca and
Taoyang Wu. Reconstructing phylogenetic level1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173200, 2017. Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/1411.6804.







Philippe Gambette,
Katharina Huber and
Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):20222048, 2017. Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness. Note: http://arxiv.org/abs/1511.08387.



Julia Matsieva,
Steven Kelk,
Celine Scornavacca,
Chris Whidden and
Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404417, 2017. Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.







Sha Zhu and
James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283298, 2017. Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybridcoal, Program HybridLambda, Program PhyloNet, software, uniqueness. Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.



Misagh Kordi and
Mukul S. Bansal. On the Complexity of DuplicationTransferLoss Reconciliation with NonBinary Gene Trees. In TCBB, Vol. 14(3):587599, 2017. Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.



Andreas Gunawan,
Bhaskar DasGupta and
Louxin Zhang. A decomposition theorem and two algorithms for reticulationvisible networks. In Information and Computation, Vol. 252:161175, 2017. Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.





Bingxin Lu,
Louxin Zhang and
Hon Wai Leong. A program to compute the soft RobinsonFoulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017. Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program iceluPhyloNetwork. Note: http://dx.doi.org/10.1186/s1286401735005.





Magnus Bordewich,
Simone Linz and
Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:112, 2017. Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulationvisible network, SPR distance, treebased network, treechild network. Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.



Celine Scornavacca,
Joan Carles Pons and
Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129137, 2017. Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.



Jesper Jansson,
Ramesh Rajaby and
WingKin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115126 of LNCS, Springer, 2017. Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance. Note: .



Leo van Iersel,
Vincent Moulton,
Eveline De Swart and
Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):11351154, 2017. Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1007/s1153801702754.



Philippe Gambette,
Leo van Iersel,
Mark Jones,
Manuel Lafond,
Fabio Pardi and
Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.121, 2017. Keywords: distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance. Note: https://halupecupem.archivesouvertes.fr/hal01572624/en/.





Han Lai,
Maureen Stolzer and
Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMBCG17, Vol. 10562:298320 of LNCS, Springer, 2017. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.



Claudia SolísLemus,
Paul Bastide and
Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, Vol. 34(12):32923298, 2017. Keywords: from sequences, from trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, software. Note: https://doi.org/10.1093/molbev/msx235.





Klaus Schliep,
Alastair J. Potts,
David A. Morrison and
Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):12121220, 2017. Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization. Note: http://dx.doi.org/10.1111/2041210X.12760.







Edwin Jacox,
Mathias Weller,
Eric Tannier and
Celine Scornavacca. Resolution and reconciliation of nonbinary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980987, 2017. Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btw778.









Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017. Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model. Note: https://tel.archivesouvertes.fr/tel01629648/en/, slides..





KuangYu Chang,
Yun Cui,
SiuMing Yiu and
WingKai Hon. Reconstructing OneArticulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:3445 of LNCS, Springer, 2017. Keywords: explicit network, from distances, kreticulated, phylogenetic network, phylogeny, reconstruction. Note: https://link.springer.com/content/pdf/10.1007%2F9783319595757.pdf#page=100.








Leo van Iersel,
Steven Kelk,
Nela Lekic,
Chris Whidden and
Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):16071631, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1402.2136.



Katharina Huber,
Vincent Moulton,
Mike Steel and
Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):17611780, 2016. Keywords: compressed network, explicit network, FUstable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network. Note: http://arxiv.org/abs/1506.04438.





Steven Kelk,
Leo van Iersel,
Celine Scornavacca and
Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189215, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction. Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.





Andreas Gunawan,
Bhaskar DasGupta and
Louxin Zhang. Locating a Tree in a ReticulationVisible Network in Cubic Time. In RECOMB16, Vol. 9649:266 of LNBI, Springer, 2016. Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulationvisible network, tree containment. Note: http://arxiv.org/abs/1507.02119.



Sajad Mirzaei and
Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565570, 2016. Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software. Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNspreprint.pdf.



Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197208 of LNCS, springer, 2016. Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://halupecupem.archivesouvertes.fr/hal01226035 .







Vincent Ranwez,
Celine Scornavacca,
JeanPhilippe Doyon and
Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):18111844, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.





François Chevenet,
JeanPhilippe Doyon,
Celine Scornavacca,
Edwin Jacox,
Emmanuelle Jousselin and
Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608610, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization. Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.









Maria Anaya,
Olga AnipchenkoUlaj,
Aisha Ashfaq,
Joyce Chiu,
Mahedi Kaiser,
Max Shoji Ohsawa,
Megan Owen,
Ella Pavlechko,
Katherine St. John,
Shivam Suleria,
Keith Thompson and
Corrine Yap. On Determining if Treebased Networks Contain Fixed Trees. In BMB, Vol. 78(5):961969, 2016. Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, treebased network. Note: http://arxiv.org/abs/1602.02739.







James Oldman,
Taoyang Wu,
Leo van Iersel and
Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):21512162, 2016. Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.















Philippe Gambette,
Leo van Iersel,
Steven Kelk,
Fabio Pardi and
Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):17731795, 2016. Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudopolynomial, time consistent network, tree containment, tree sibling network. Note: http://arxiv.org/abs/1607.06285.



Hussein A. Hejase and
Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):112, 2016. Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network. Note: http://dx.doi.org/10.1186/s1285901612771.











Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016. Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey. Note: http://dx.doi.org/10.1371/journal.pone.0165834.





Leo van Iersel,
Steven Kelk and
Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):10751089, 2016. Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction. Note: https://arxiv.org/abs/1311.4045v3.





Edwin Jacox,
Cédric Chauve,
Gergely J. Szöllösi,
Yann Ponty and
Celine Scornavacca. EcceTERA: comprehensive gene treespecies tree reconciliation using parsimony. In BIO, Vol. 32(13):20562058, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA. Note: https://doi.org/10.1093/bioinformatics/btw105.





Monika Balvociute. Flat Embeddings of Genetic and Distance Data. PhD thesis, University of Otago, 2016. Keywords: abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network. Note: http://hdl.handle.net/10523/6286.








Mareike Fischer,
Leo van Iersel,
Steven Kelk and
Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559585, 2015. 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. Note: http://arxiv.org/abs/1302.2430.







Katharina Huber,
Leo van Iersel,
Vincent Moulton and
Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102111, 2015. Keywords: explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://dx.doi.org/10.1093/sysbio/syu076.







Philippe Gambette,
Andreas Gunawan,
Anthony Labarre,
Stéphane Vialette and
Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96107 of LNCS, Springer, 2015. Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearlystable network, phylogenetic network, phylogeny, polynomial, tree containment. Note: https://hal.archivesouvertes.fr/hal01116231/en.







Quan Nguyen and
Teemu Roos. Likelihoodbased inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126140 of LNCS, springer, 2015. Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software. Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.





Jittat Fakcharoenphol,
Tanee Kumpijit and
Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337342, IEEE, 2015. Keywords: dynamic programming, explicit network, from network, from rooted trees, nearlystable network, phylogenetic network, phylogeny, polynomial, tree containment.



Misagh Kordi and
Mukul S. Bansal. On the Complexity of DuplicationTransferLoss Reconciliation with NonBinary Gene Trees. In ISBRA15, Vol. 9096:187198 of LNCS, springer, 2015. Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf.



Yun Yu and
Luay Nakhleh. A DistanceBased Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378389 of LNCS, springer, 2015. Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction. Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhlehISBRA15.pdf.



Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. In BMCB, Vol. 16(236):115, 2015. Keywords: agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction. Note: http://dx.doi.org/10.1186/s1285901506607.







Maxime Morgado. Propriétés structurelles et relations des classes de réseaux phylogénétiques. Master's thesis, ENS Cachan, 2015. Keywords: compressed network, distinctcluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, treebased network, treechild network, unicyclic network.



Yun Yu and
Luay Nakhleh. A maximum pseudolikelihood approach for phylogenetic networks. In RECOMBCG15, Vol. 16(Suppl 10)(S10):110 of BMC Genomics, BioMed Central, 2015. Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance. Note: http://dx.doi.org/10.1186/1471216416S10S10.



Sha Zhu,
James H. Degnan,
Sharyn J. Goldstein and
Bjarki Eldon. HybridLambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):17, 2015. Keywords: explicit network, from network, phylogenetic network, phylogeny, Program HybridLambda, simulation, software. Note: http://dx.doi.org/10.1186/s128590150721y.



Gergely J. Szöllösi,
Adrián Arellano Davín,
Eric Tannier,
Vincent Daubin and
Bastien Boussau. Genomescale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):111, 2015. Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction. Note: http://dx.doi.org/10.1098/rstb.2014.0335.









Marc Thuillard and
Didier FraixBurnet. Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers? In Evolutionary Bioinformatics, Vol. 11:213221, 2015. [Abstract] Keywords: circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split. Note: http://dx.doi.org/10.4137%2FEBO.S28158.











Jessica W. Leigh and
David Bryant. PopART: fullfeature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):11101116, 2015. Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software. Note: http://dx.doi.org/10.1111/2041210X.12410.



Gabriel Cardona,
Joan Carles Pons and
Francesc Rosselló. A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. In ALMOB, Vol. 10(28):115, 2015. Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, treebased network. Note: http://dx.doi.org/10.1186/s130150150059z.








Steven Kelk and
Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886915, 2014. Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1108.3653.
Toggle abstract
"Here we show that, given a set of clusters C on a set of taxa X, where X=n, it is possible to determine in time f(k)×poly(n) whether there exists a level≤k network (i.e. a network where each biconnected component has reticulation number at most k) that represents all the clusters in C in the softwired sense, and if so to construct such a network. This extends a result from Kelk et al. (in IEEE/ACM Trans. Comput. Biol. Bioinform. 9:517534, 2012) which showed that the problem is polynomialtime solvable for fixed k. By defining "kreticulation generators" analogous to "levelk generators", we then extend this fixed parameter tractability result to the problem where k refers not to the level but to the reticulation number of the whole network. © 2012 Springer Science+Business Media New York."



Hadi Poormohammadi,
Changiz Eslahchi and
Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014. Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software. Note: http://arxiv.org/abs/1201.3722.
Toggle abstract
"The problem of constructing an optimal rooted phylogenetic network from an arbitrary set of rooted triplets is an NPhard problem. In this paper, we present a heuristic algorithm called TripNet, which tries to construct a rooted phylogenetic network with the minimum number of reticulation nodes from an arbitrary set of rooted triplets. Despite of current methods that work for dense set of rooted triplets, a key innovation is the applicability of TripNet to nondense set of rooted triplets. We prove some theorems to clarify the performance of the algorithm. To demonstrate the efficiency of TripNet, we compared TripNet with SIMPLISTIC. It is the only available software which has the ability to return some rooted phylogenetic network consistent with a given dense set of rooted triplets. But the results show that for complex networks with high levels, the SIMPLISTIC running time increased abruptly. However in all cases TripNet outputs an appropriate rooted phylogenetic network in an acceptable time. Also we tetsed TripNet on the Yeast data. The results show that Both TripNet and optimal networks have the same clustering and TripNet produced a level3 network which contains only one more reticulation node than the optimal network."





Leo van Iersel and
Vincent Moulton. Trinets encode treechild and level2 phylogenetic networks. In JOMB, Vol. 68(7):17071729, 2014. Keywords: explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1210.0362.
Toggle abstract
"Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level1 phylogenetic networks are encoded by their trinets, and also conjectured that all "recoverable" rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level2 networks and binary treechild networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets. © 2013 SpringerVerlag Berlin Heidelberg."



Leo van Iersel,
Steven Kelk,
Nela Lekic and
Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):4966, 2014. Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1210.3211.
Toggle abstract
"Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest (maf) problem asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic Agreement Forest (maaf) problem has the additional restriction that the components of the forest cannot have conflicting ancestral relations in the input trees. There has been considerable interest in the special cases of these problems in which the input trees are required to be binary. However, in practice, phylogenetic trees are rarely binary, due to uncertainty about the precise order of speciation events. Here, we show that the general, nonbinary version of maf has a polynomialtime 4approximation and a fixedparameter tractable (exact) algorithm that runs in O(4opoly(n)) time, where n = X and k is the number of components of the agreement forest minus one. Moreover, we show that a capproximation algorithm for nonbinary maf and a dapproximation algorithm for the classical problem Directed Feedback Vertex Set (dfvs) can be combined to yield a d(c+3)approximation for nonbinary maaf. The algorithms for maf have been implemented and made publicly available. © 2014 Society for Industrial and Applied Mathematics."



Anthony Labarre and
Sicco Verwer. Merging partially labelled trees: hardness and a declarative programming solution. In TCBB, Vol. 11(2):389397, 2014. Keywords: abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction. Note: https://halupecupem.archivesouvertes.fr/hal00855669.
Toggle abstract
"Intraspecific studies often make use of haplotype networks instead of gene genealogies to represent the evolution of a set of genes. Cassens et al. proposed one such network reconstruction method, based on the global maximum parsimony principle, which was later recast by the first author of the present work as the problem of finding a minimum common supergraph of a set of t partially labelled trees. Although algorithms have been proposed for solving that problem on two graphs, the complexity of the general problem on trees remains unknown. In this paper, we show that the corresponding decision problem is NPcomplete for t=3. We then propose a declarative programming approach to solving the problem to optimality in practice, as well as a heuristic approach, both based on the idpsystem, and assess the performance of both methods on randomly generated data. © 20042012 IEEE."





Leo van Iersel and
Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299311 of LNCS, springer, 2014. Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction. Note: http://arxiv.org/abs/1311.4045.



Jesper Jansson and
Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:6678, 2014. Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.
Toggle abstract
"We consider a generalization of the rooted triplet distance between two phylogenetic trees to two phylogenetic networks. We show that if each of the two given phylogenetic networks is a socalled galled tree with n leaves then the rooted triplet distance can be computed in o(n2.687) time. Our upper bound is obtained by reducing the problem of computing the rooted triplet distance between two galled trees to that of counting monochromatic and almostmonochromatic triangles in an undirected, edgecolored graph. To count different types of colored triangles in a graph efficiently, we extend an existing technique based on matrix multiplication and obtain several new algorithmic results that may be of independent interest: (i) the number of triangles in a connected, undirected, uncolored graph with m edges can be computed in o(m1.408) time; (ii) if G is a connected, undirected, edgecolored graph with n vertices and C is a subset of the set of edge colors then the number of monochromatic triangles of G with colors in C can be computed in o(n2.687) time; and (iii) if G is a connected, undirected, edgecolored graph with n vertices and R is a binary relation on the colors that is computable in O(1) time then the number of Rchromatic triangles in G can be computed in o(n2.687) time. © 2013 Elsevier B.V. All rights reserved."



Ward C Wheeler. Phyletic groups on networks. In Cladistics, Vol. 30(4):447451, 2014. Keywords: explicit network, from network, phylogenetic network, phylogeny. Note: http://dx.doi.org/10.1111/cla.12062.
Toggle abstract
"Three additional phyletic group types, "periphyletic," "epiphyletic", and "anaphyletic" (in addition to Hennigian mono, para, and polyphyletic) are defined in terms of trees and phylogenetic networks (trees with directed reticulate edges) via a generalization of the algorithmic definitions of Farris. These designations concern groups defined as monophyletic on trees, but with additional gains or losses of members from network edges. These distinctions should be useful in discussion of systems with nonvertical inheritance such as recombination between viruses, horizontal exchange between bacteria, hybridization in plants and animals, as well as human linguistic evolution. Examples are illustrated with IndoEuropean language groups. © The Willi Hennig Society 2013."



Sarah Bastkowski,
Andreas Spillner and
Vincent Moulton. Fishing for minimum evolution trees with NeighborNets. In IPL, Vol. 114(12):318, 2014. Keywords: circular split system, from distances, NeighborNet, phylogeny, polynomial.
Toggle abstract
"In evolutionary biology, biologists commonly use a phylogenetic tree to represent the evolutionary history of some set of species. A common approach taken to construct such a tree is to search through the space of all possible phylogenetic trees on the set so as to find one that optimizes some score function, such as the minimum evolution criterion. However, this is hampered by the fact that the space of phylogenetic trees is extremely large in general. Interestingly, an alternative approach, which has received somewhat less attention in the literature, is to instead search for trees within some set of bipartitions or splits of the set of species in question. Here we consider the problem of searching through a set of splits that is circular. Such sets can, for example, be generated by the NeighborNet algorithm for constructing phylogenetic networks. More specifically, we present an O(n4) time algorithm for finding an optimal minimum evolution tree in a circular set of splits on a set of species of size n. In addition, using simulations, we compare the performance of this algorithm when applied to NeighborNet output with that of FastME, a leading method for searching for minimum evolution trees in tree space. We find that, even though a circular set of splits represents just a tiny fraction of the total number of possible splits of a set, the trees obtained from circular sets compare quite favorably with those obtained with FastME, suggesting that the approach could warrant further investigation. © 2013 Elsevier B.V."



Lavanya Kannan and
Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303319, 2014. Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Toggle abstract
"Scoring a given phylogenetic network is the first step that is required in searching for the best evolutionary framework for a given dataset. Using the principle of maximum parsimony, we can score phylogenetic networks based on the minimum number of state changes across a subset of edges of the network for each character that are required for a given set of characters to realize the input states at the leaves of the networks. Two such subsets of edges of networks are interesting in light of studying evolutionary histories of datasets: (i) the set of all edges of the network, and (ii) the set of all edges of a spanning tree that minimizes the score. The problems of finding the parsimony scores under these two criteria define slightly different mathematical problems that are both NPhard. In this article, we show that both problems, with scores generalized to adding substitution costs between states on the endpoints of the edges, can be solved exactly using dynamic programming. We show that our algorithms require O(mpk) storage at each vertex (per character), where k is the number of states the character can take, p is the number of reticulate vertices in the network, m = k for the problem with edge set (i), and m = 2 for the problem with edge set (ii). This establishes an O(nmpk2) algorithm for both the problems (n is the number of leaves in the network), which are extensions of Sankoff's algorithm for finding the parsimony scores for phylogenetic trees. We will discuss improvements in the complexities and show that for phylogenetic networks whose underlying undirected graphs have disjoint cycles, the storage at each vertex can be reduced to O(mk), thus making the algorithm polynomial for this class of networks. We will present some properties of the two approaches and guidance on choosing between the criteria, as well as traverse through the network space using either of the definitions. We show that our methodology provides an effective means to study a wide variety of datasets. © Copyright 2014, Mary Ann Liebert, Inc. 2014."



Jialiang Yang,
Stefan Grünewald,
Yifei Xu and
XiuFeng Wan. Quartetbased methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014. Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction. Note: http://dx.doi.org/10.1186/17520509821
.
Toggle abstract
"Background: Phylogenetic networks are employed to visualize evolutionary relationships among a group of nucleotide sequences, genes or species when reticulate events like hybridization, recombination, reassortant and horizontal gene transfer are believed to be involved. In comparison to traditional distancebased methods, quartetbased methods consider more information in the reconstruction process and thus have the potential to be more accurate.Results: We introduce QuartetSuite, which includes a set of new quartetbased methods, namely QuartetS, QuartetA, and QuartetM, to reconstruct phylogenetic networks from nucleotide sequences. We tested their performances and compared them with other popular methods on two simulated nucleotide sequence data sets: one generated from a tree topology and the other from a complicated evolutionary history containing three reticulate events. We further validated these methods to two real data sets: a bacterial data set consisting of seven concatenated genes of 36 bacterial species and an influenza data set related to recently emerging H7N9 low pathogenic avian influenza viruses in China.Conclusion: QuartetS, QuartetA, and QuartetM have the potential to accurately reconstruct evolutionary scenarios from simple branching trees to complicated networks containing many reticulate events. These methods could provide insights into the understanding of complicated biological evolutionary processes such as bacterial taxonomy and reassortant of influenza viruses. © 2014 Yang et al.; licensee BioMed Central Ltd."



Kevin J. Liu,
Jingxuan Dai,
Kathy Truong,
Ying Song,
Michael H. Kohn and
Luay Nakhleh. An HMMBased Comparative Genomic Framework for Detecting Introgression in Eukaryotes. In PLoS ONE, Vol. 10(6):e1003649, 2014. Keywords: explicit network, from network, phylogenetic network, phylogeny, Program PhyloNetHMM. Note: http://arxiv.org/abs/1310.7989.
Toggle abstract
"One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNetHMMa new comparative genomic framework for detecting introgression in genomes. PhyloNetHMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism. © 2014 Liu et al."











Vladimir Makarenkov,
Alix Boc and
Pierre Legendre. A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers. In
Fuad Aleskerov,
Boris Goldengorin and
Panos M. Pardalos editors, Clusters, Orders, and Trees: Methods and Applications, Vol. 92 of Springer Optimization and Its Applications, Springer, 2014. Keywords: explicit network, phylogenetic network, phylogeny, reconstruction.



Ran LibeskindHadas,
YiChieh Wu,
Mukul S. Bansal and
Manolis Kellis. Paretooptimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87i95 of BIO, 2014. Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btu289.
Toggle abstract
"Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. Results: We address this problem by giving an efficient algorithm for computing Paretooptimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. © 2014 The Author. Published by Oxford University Press. All rights reserved."



Leo van Iersel,
Steven Kelk,
Nela Lekic and
Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. In BMCB, Vol. 15(127):112, 2014. Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, Program CycleKiller, Program TerminusEst, reconstruction. Note: http://dx.doi.org/10.1186/1471210515127.



YiChieh Wu. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species. PhD thesis, Massachusetts Institute of Technology, U.S.A., 2014. Keywords: duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFixDTL, reconstruction. Note: http://hdl.handle.net/1721.1/87937.



Monika Balvociute,
Andreas Spillner and
Vincent Moulton. FlatNJ: A Novel NetworkBased Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383396, 2014. Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network. Note: http://dx.doi.org/10.1093/sysbio/syu001.
Toggle abstract
"Split networks are a type of phylogenetic network that allow visualization of conflict in evolutionary data. We present a new method for constructing such networks called FlatNetJoining (FlatNJ). A key feature of FlatNJ is that it produces networks that can be drawn in the plane in which labels may appear inside of the network. For complex data sets that involve, for example, nonneutral molecular markers, this can allow additional detail to be visualized as compared to previous methods such as split decomposition and NeighborNet. We illustrate the application of FlatNJ by applying it to whole HIV genome sequences, where recombination has taken place, fluorescent proteins in corals, where ancestral sequences are present, and mitochondrial DNA sequences from gall wasps, where biogeographical relationships are of interest. We find that the networks generated by FlatNJ can facilitate the study of genetic variation in the underlying molecular sequence data and, in particular, may help to investigate processes such as intralocus recombination. FlatNJ has been implemented in Java and is freely available at www.uea.ac.uk/computing/software/ flatnj. [flat split system; NeighborNet; Phylogenetic network; QNet; split; split network.] © The Author(s) 2014."







Zhijiang Li. FixedParameter Algorithm for Hybridization Number of Two Multifurcating Trees. Master's thesis, Dalhousie University, Canada, 2014. Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction. Note: http://hdl.handle.net/10222/53976.



Matthieu Willems,
Nadia Tahiri and
Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the NeighborJoining principle. In JBCB, Vol. 12(5), 2014. Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
Toggle abstract
"Several algorithms and software have been developed for inferring phylogenetic trees. However, there exist some biological phenomena such as hybridization, recombination, or horizontal gene transfer which cannot be represented by a tree topology. We need to use phylogenetic networks to adequately represent these important evolutionary mechanisms. In this article, we present a new efficient heuristic algorithm for inferring hybridization networks from evolutionary distance matrices between species. The famous NeighborJoining concept and the leastsquares criterion are used for building networks. At each step of the algorithm, before joining two given nodes, we check if a hybridization event could be related to one of them or to both of them. The proposed algorithm finds the exact tree solution when the considered distance matrix is a tree metric (i.e. it is representable by a unique phylogenetic tree). It also provides very good hybrids recovery rates for large trees (with 32 and 64 leaves in our simulations) for both distance and sequence types of data. The results yielded by the new algorithm for real and simulated datasets are illustrated and discussed in detail. © Imperial College Press."



Paul Cordue,
Simone Linz and
Charles Semple. Phylogenetic Networks that Display a Tree Twice. In BMB, Vol. 76(10):26642679, 2014. Keywords: from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, treechild network. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf.
Toggle abstract
"In the last decade, the use of phylogenetic networks to analyze the evolution of species whose past is likely to include reticulation events, such as horizontal gene transfer or hybridization, has gained popularity among evolutionary biologists. Nevertheless, the evolution of a particular gene can generally be described without reticulation events and therefore be represented by a phylogenetic tree. While this is not in contrast to each other, it places emphasis on the necessity of algorithms that analyze and summarize the treelike information that is contained in a phylogenetic network. We contribute to the toolbox of such algorithms by investigating the question of whether or not a phylogenetic network embeds a tree twice and give a quadratictime algorithm to solve this problem for a class of networks that is more general than treechild networks. © 2014, Society for Mathematical Biology."













Joel Sjöstrand,
Ali Tofigh,
Vincent Daubin,
Lars Arvestad,
Bengt Sennblad and
Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409420, 2014. Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIMEDLTRS, reconstruction. Note: http://dx.doi.org/10.1093/sysbio/syu007.



Adrià Alcalà Mena,
Mercè Llabrés,
Francesc Rosselló and
Pau Rullan. TreeChild Cluster Networks. In Fundamenta Informaticae, Vol. 134(12):115, 2014. Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program PhyloNetwork, reconstruction, treechild network.










Katharina Huber and
Vincent Moulton. Encoding and Constructing 1Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714738, 2013. Keywords: explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/abs/1110.0728.
Toggle abstract
"Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or nontreelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or encode the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, wellstudied type of phylogenetic network called a 1nested network, the trinets displayed by a 1nested network always encode the network. We also present an efficient algorithm for deciding whether a dense set of trinets (i.e. one that contains a trinet on every 3element subset of a set) can be displayed by a 1nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks. © 2012 Springer Science+Business Media, LLC."



Leo van Iersel and
Simone Linz. A quadratic kernel for computing the hybridization number of multiple trees. In IPL, Vol. 113:318323, 2013. Keywords: explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction. Note: http://arxiv.org/abs/1203.4067, poster.
Toggle abstract
"It has recently been shown that the NPhard problem of calculating the minimum number of hybridization events that is needed to explain a set of rooted binary phylogenetic trees by means of a hybridization network is fixedparameter tractable if an instance of the problem consists of precisely two such trees. In this paper, we show that this problem remains fixedparameter tractable for an arbitrarily large set of rooted binary phylogenetic trees. In particular, we present a quadratic kernel. © 2013 Elsevier B.V."



Chris Whidden,
Robert G. Beiko and
Norbert Zeh. FixedParameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):14311466, 2013. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance. Note: http://arxiv.org/abs/1108.2664, slides.
Toggle abstract
"We present new and improved fixedparameter algorithms for computing maximum agreement forests of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree pruneandregraft distance and, if the agreement forest is acyclic, to their hybridization number. These distance measures are essential tools for understanding reticulate evolution. Our algorithm for computing maximum acyclic agreement forests is the first depthbounded search algorithm for this problem. Our algorithms substantially outperform the best previous algorithms for these problems. © 2013 Society for Industrial and Applied Mathematics."



Stefan Grünewald,
Andreas Spillner,
Sarah Bastkowski,
Anja Bögershausen and
Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151160, 2013. Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.
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"Supertrees are a commonly used tool in phylogenetics to summarize collections of partial phylogenetic trees. As a generalization of supertrees, phylogenetic supernetworks allow, in addition, the visual representation of conflict between the trees that is not possible to observe with a single tree. Here, we introduce SuperQ, a new method for constructing such supernetworks (SuperQ is freely available at >www.uea.ac.uk/computing/superq.). It works by first breaking the input trees into quartet trees, and then stitching these together to form a special kind of phylogenetic network, called a split network. This stitching process is performed using an adaptation of the QNet method for split network reconstruction employing a novel approach to use the branch lengths from the input trees to estimate the branch lengths in the resulting network. Compared with previous supernetwork methods, SuperQ has the advantage of producing a planar network. We compare the performance of SuperQ to the Zclosure and Qimputation supernetwork methods, and also present an analysis of some published data sets as an illustration of its applicability. © 20042012 IEEE."



Teresa Piovesan and
Steven Kelk. A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees. In TCBB, Vol. 10(1):1825, 2013. Keywords: FPT, from rooted trees, phylogenetic network, phylogeny, Program TerminusEst, reconstruction. Note: http://arxiv.org/abs/1207.6090.
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"Here, we present a new fixed parameter tractable algorithm to compute the hybridization number (r) of two rooted, not necessarily binary phylogenetic trees on taxon set (X) in time ((6r r) · poly(n)), where (n= X). The novelty of this approach is its use of terminals, which are maximal elements of a natural partial order on (X), and several insights from the softwired clusters literature. This yields a surprisingly simple and practical boundedsearch algorithm and offers an alternative perspective on the underlying combinatorial structure of the hybridization number problem. © 20042012 IEEE."



 
