On the Balanced Minimum Evolution polytope

Discrete Optimization - Tập 36 - Trang 100570 - 2020
Daniele Catanzaro1,2, Raffaele Pesenti3, Laurence A. Wolsey1
1Center for Operations Research and Econometrics (CORE), Université Catholique de Louvain, Voie du Roman Pays 34, B-1348, Louvain-la-Neuve, Belgium
2Luxembourg Institute of Socio-Economic Research (LISER), 11 Porte des Sciences, L-4366 Esch-sur-Alzette, Luxembourg
3Department of Management, Università Ca’ Foscari, San Giobbe, Cannaregio 837, I-30121 Venezia, Italy

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Tài liệu tham khảo

Felsenstein, 2004

Catanzaro, 2011, Estimating phylogenies from molecular data, 149

Catanzaro, 2012, The balanced minimum evolution problem, INFORMS J. Comput., 24, 276, 10.1287/ijoc.1110.0455

Rinnooy Kan, 1978, The complexity of the network design problem, Networks, 8, 279, 10.1002/net.3230080402

Pauplin, 2000, Direct calculation of a tree length using a distance matrix, J. Mol. Evol., 51, 41, 10.1007/s002390010065

Desper, 2004, Theoretical foundations of the balanced minimum evolution method of phylogenetic inference and its relationship to the weighted least-squares tree fitting, Mol. Biol. Evol., 21, 587, 10.1093/molbev/msh049

Gascuel, 2006, Neighbor-joining revealed, Mol. Biol. Evol., 23, 1997, 10.1093/molbev/msl072

Fiorini, 2012, Approximating the balanced minimum evolution problem, Oper. Res. Lett., 40, 31, 10.1016/j.orl.2011.10.003

Aringhieri, 2011, Optimal solutions for the balanced minimum evolution problem, Comput. Oper. Res., 38, 1845, 10.1016/j.cor.2011.02.020

Pardi, 2009

Catanzaro, 2009, The minimum evolution problem: Overview and classification, Networks, 53, 112, 10.1002/net.20280

Gascuel, 2005

Huffman, 1952, A method for the construction of minimum redundancy codes

Parker, 1996, The construction of Huffman codes is a submodular (“convex”) optimization problem over a lattice of binary trees, SIAM J. Comput., 28, 1875, 10.1137/S0097539796311077

Sayood, 2017

Eickmeyer, 2008, On the optimality of the neighbor-joining algorithm, Algorithms Mol. Biol., 3, 1

Haws, 2011, Optimality of the neighbor joining algorithm and faces of the balanced minimum evolution polytope, Bull. Math. Biol., 73, 2627, 10.1007/s11538-011-9640-x

Forcey, 2016, Facets of the balanced minimal evolution polytope, J. Math. Biol., 73, 447, 10.1007/s00285-015-0957-1

Gawrilow, 2000, Polymake: A framework for analyzing convex polytopes, 43

Billera, 2001, Geometry of the space of phylogenetic trees, Adv. Appl. Math., 27, 733, 10.1006/aama.2001.0759

Forcey, 2017, Split-facets for balanced minimal evolution polytopes and the permutoassociahedron, Bull. Math. Biol., 79, 975, 10.1007/s11538-017-0264-7

Kapranov, 1993, The permutoassociahedron, Mac Lane’s coherence theorem and asymptotic zones for the KZ equation, J. Pure Appl. Algebra, 85, 119, 10.1016/0022-4049(93)90049-Y

Reiner, 1993

Buneman, 1971, The recovery of trees from measure of dissimilarities, 387

Erdös, 1999, A few logs suffice to build (almost) all trees: Part I, Random Struct. Algorithms, 14, 153, 10.1002/(SICI)1098-2418(199903)14:2<153::AID-RSA3>3.0.CO;2-R

Waterman, 1977, Additive evolutionary trees, J. Theoret. Biol., 64, 199, 10.1016/0022-5193(77)90351-4

Nemhauser, 1999

Wolfram Research, Inc. Mathematica, Version 11.3. Champaign, IL, 2018.

Reinhard, 2005