Arc-Completion of 2-Colored Best Match Graphs to Binary-Explainable Best Match Graphs

被引：2

作者：

Schaller, David ^{[1
,2
,3
]}

Geiss, Manuela ^{[4
]}

Hellmuth, Marc ^{[5
]}

Stadler, Peter F. ^{[1
,2
,3
,6
,7
,8
,9
,10
]}

机构：

[1] Max Planck Inst Math Sci, D-04103 Leipzig, Germany

[2] Univ Leipzig, Bioinformat Grp, Dept Comp Sci, D-04107 Leipzig, Germany

[3] Univ Leipzig, Interdisciplinary Ctr Bioinformat, D-04107 Leipzig, Germany

[4] Software Competence Ctr Hagenberg GmbH SCCH, A-4232 Hagenberg, Austria

[5] Stockholm Univ, Fac Sci, Dept Math, SE-10691 Stockholm, Sweden

[6] Univ Leipzig, Competence Ctr Scalable Data Serv & Solut, Leipzig Res Ctr Civilizat Dis, Res iDiv Halle Jena Leipzig,German Ctr Integrat B, D-04103 Leipzig, Germany

[7] Univ Leipzig, Leipzig Res Ctr Civilizat Dis LIFE, D-04103 Leipzig, Germany

[8] Univ Vienna, Inst Theoret Chem, A-1090 Vienna, Austria

[9] Univ Nacl Colombia, Fac Ciencias, CO-111321 Bogota, Colombia

[10] Santa Fe Inst, Santa Fe, NM 87501 USA

来源：

ALGORITHMS | 2021年 / 14卷 / 04期

关键词：

best matches; least resolved trees; graph completion; polynomial-time algorithm; SPECIATION; COMPLEXITY;

D O I：

10.3390/a14040110

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

Best match graphs (BMGs) are vertex-colored digraphs that naturally arise in mathematical phylogenetics to formalize the notion of evolutionary closest genes w.r.t. an a priori unknown phylogenetic tree. BMGs are explained by unique least resolved trees. We prove that the property of a rooted, leaf-colored tree to be least resolved for some BMG is preserved by the contraction of inner edges. For the special case of two-colored BMGs, this leads to a characterization of the least resolved trees (LRTs) of binary-explainable trees and a simple, polynomial-time algorithm for the minimum cardinality completion of the arc set of a BMG to reach a BMG that can be explained by a binary tree.

引用

页数：10

共 16 条

[1] The structure of 2-colored best match graphs
Korchmaros, Annachiara
[J]. DISCRETE APPLIED MATHEMATICS, 2021, 304 : 397 - 416
[2] Best Match Graphs With Binary Trees
Schaller, David
Geiss, Manuela
Hellmuth, Marc
Stadler, Peter F. F.
[J]. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2023, 20 (03) : 1679 - 1690
[3] Best match graphs
Geiss, Manuela
Chavez, Edgar
Gonzalez Laffitte, Marcos
Lopez Sanchez, Alitzel
Stadler, Baerbel M. R.
Valdivia, Dulce I.
Hellmuth, Marc
Hernandez Rosales, Maribel
Stadler, Peter F.
[J]. JOURNAL OF MATHEMATICAL BIOLOGY, 2019, 78 (07) : 2015 - 2057
[4] Best match graphs
Manuela Geiß
Edgar Chávez
Marcos González Laffitte
Alitzel López Sánchez
Bärbel M. R. Stadler
Dulce I. Valdivia
Marc Hellmuth
Maribel Hernández Rosales
Peter F. Stadler
[J]. Journal of Mathematical Biology, 2019, 78 : 2015 - 2057
[5] Reciprocal best match graphs
Manuela Geiß
Peter F. Stadler
Marc Hellmuth
[J]. Journal of Mathematical Biology, 2020, 80 : 865 - 953
[6] Corrigendum to “Best match graphs”
Schaller D.
Geiß M.
Chávez E.
González Laffitte M.
López Sánchez A.
Stadler B.M.R.
Valdivia D.I.
Hellmuth M.
Hernández Rosales M.
Stadler P.F.
[J]. Journal of Mathematical Biology, 2021, 82 (6)
[7] Reciprocal best match graphs
Geiss, Manuela
Stadler, Peter F.
Hellmuth, Marc
[J]. JOURNAL OF MATHEMATICAL BIOLOGY, 2020, 80 (03) : 865 - 953
[8] Quasi-best match graphs
Korchmaros, Annachiara
Schaller, David
Hellmuth, Marc
Stadler, Peter F.
[J]. DISCRETE APPLIED MATHEMATICS, 2023, 331 : 104 - 125
[9] Least resolved trees for two-colored best match graphs
Schaller, David
Geiß, Manuela
Hellmuth, Marc
Stadler, Peter F.
[J]. Journal of Graph Algorithms and Applications, 2021, 25 (01) : 397 - 416
[10] Complexity of modification problems for best match graphs
Schaller, David
Stadler, Peter F.
Hellmuth, Marc
[J]. THEORETICAL COMPUTER SCIENCE, 2021, 865 : 63 - 84

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