Publications related to 'heuristic'
 
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Article (Journal)
1
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Philippe Gambette and Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472-479, 2008.  
Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/.
       
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2
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Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993.  
Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software.
Note: http://dx.doi.org/10.1007/BF00182187.
       

3
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Supriya Munshaw and Thomas B. Kepler. An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics. In MBE, Vol. 25(6):1199-1208, 2008.  
Keywords: explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software.
Note: http://dx.doi.org/10.1093/molbev/msn066.
       
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Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic. In TCBB, Vol. 6(3):495-505, 2009.  
Keywords: explicit network, heuristic, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-MP.pdf.
       

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Ran Libeskind-Hadas and Michael A. Charleston. On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem. In JCB, Vol. 16(1):105-117, 2009.  
Keywords: cophylogeny, heuristic, NP complete, parsimony, phylogenetic network, reconstruction.
Note: http://dx.doi.org/10.1089/cmb.2008.0084.
       
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Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. In TCBB, Vol. 8(3):607-620, 2011.  
Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software.
Note: http://arxiv.org/abs/0910.4067.
       
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7
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Tal Dagan, Yael Artzy-Randrup and William Martin. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution. In PNAS, Vol. 105:10039-10044, 2008.  
Keywords: from sequences, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.0800679105.
       
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8
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Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010.  
Keywords: explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.
       
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9
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Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010.  
Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network.
Note: http://dx.doi.org/10.1186/1471-2148-10-254.
       
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10
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Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010.  
Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.
       

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Changiz Eslahchi, Reza Hassanzadeh, Ehsan Mottaghi, Mahnaz Habibi, Hamid Pezeshk and Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012.  
Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.
       
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12
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Reza Hassanzadeh, Changiz Eslahchi and Wing-Kin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738-744, 2012.  
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.
       
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13
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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.
       
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14
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Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen and Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 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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15
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Lavanya Kannan and Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.  
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.
       
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16
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Hadi Poormohammadi and Changiz Eslahchi. Constructing Rooted Phylogenetic Networks from Triplets based on Height Function. In International Journal of Emerging Technology and Advanced Engineering, Vol. 2(7):389-393, 2012.  
Keywords: from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.ijetae.com/files/Volume2Issue7/IJETAE_0712_67.pdf.
       

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Joseph K. Pickrell and Jonathan K. Pritchard. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. In PLoS Genetics, Vol. 8(11):e1002967, 2012.  
Keywords: explicit network, heuristic, likelihood, phylogenetic network, phylogeny, population genetics, Program TreeMix.
Note: http://dx.doi.org/10.1371/journal.pgen.1002967.
       
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18
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Thi-Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Jean-Philippe Doyon and Vincent Berry. Reconciliation and local gene tree rearrangement can be of mutual profit. In ALMOB, Vol. 8(12), 2013.  
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software.
       
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Anthony Labarre and Sicco Verwer. Merging partially labelled trees: hardness and a declarative programming solution. In TCBB, Vol. 11(2):389-397, 2014.  
Keywords: abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-00855669.
       
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Juan Wang. A new algorithm to construct phylogenetic networks from trees. In Genetics and Molecular Research, Vol. 13(1):1456-1464, 2014.  
Keywords: explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction.
Note: http://dx.doi.org/10.4238/2014.March.6.4.
       
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Matthieu Willems, Nadia Tahiri and Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. In JBCB, Vol. 12(5), 2014.  
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
       
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Sajad Mirzaei and Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016.  
Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software.
Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.
       

InProceedings
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Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:61-72 of LNCS, springer, 2007.  
Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal.
Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf.
       

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Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005.  
Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.
       

25
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Hyun Jung Park, Guohua Jin and Luay Nakhleh. Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees. In CSB10, 2010.  
Keywords: bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf.
       

26
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Celine Scornavacca, Franziska Zickmann and Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248-i256 of BIO, 2011.  
Keywords: from network, heuristic, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
       
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27
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Hyun Jung Park and Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213-224 of LNCS, springer, 2012.  
Keywords: explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software.
Note: https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf.
       
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28
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Changiz Eslahchi and Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106-107, 2011.  
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network.
Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.
       

29
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Hyun Jung Park and Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria. In RECOMB-CG'12, Vol. 13(suppl 19):S12 of BMCB, 2012.  
Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.biomedcentral.com/1471-2105/13/S19/S12.
       

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Thi-Hau Nguyen, Jean-Philippe Doyon, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Vincent Ranwez and Vincent Berry. Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference. In WABI12, Vol. 7534:123-134 of LNCS, springer, 2012.  
Keywords: duplication, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, reconstruction.
Note: http://hal.archives-ouvertes.fr/hal-00718347/en/.
       
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31
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Yun Yu, Nikola Ristic and Luay Nakhleh. Fast algorithms and heuristics for phylogenomics under ILS and hybridization. In RECOMB-CG'13, Vol. 14(Suppl 15):S6 of BMCB, 2013.  
Keywords: from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       

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Yun Yu and Luay Nakhleh. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378-389 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/YuNakhleh-ISBRA15.pdf.
       

MastersThesis
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Derek Ruths. Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer. Master's thesis, Rice University, U.S.A., 2005.  
Keywords: explicit network, from rooted trees, from species tree, heuristic, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://hdl.handle.net/1911/17912.
       

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Matthieu Willems. Un nouvel algorithme pour l'inférence de réseaux d'hybridation. Master's thesis, Université du Québec à Montréal, Canada, 2012.  
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.archipel.uqam.ca/5015/.
       

PhdThesis
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Thi-Hau Nguyen. Réconciliations: corriger des arbres de gènes et inférer la fiabilité des événements évolutifs. PhD thesis, Université Montpellier 2, France, 2013.  
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, reconstruction.
       

Misc
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Ruzbeh Tusserkani, Changiz Eslahchi, Hadi Poormohammadi and Azin Azadi. TripNet: A Method for Constructing Phylogenetic Networks from Triplets. 2011.  
Keywords: explicit network, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1104.4720.
       

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Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. FastNet: Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data. 2017.  
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: http://biorxiv.org/content/early/2017/05/01/132795.