{"title":"The Computational Complexity of the ChordLink Model","authors":"Philipp Kindermann, Jan Sauer, Alexander Wolff","doi":"10.7155/jgaa.00643","DOIUrl":"https://doi.org/10.7155/jgaa.00643","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"87 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135611251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Guest Editors' Foreword","authors":"Patrizio Angelini, Reinhard von Hanxleden","doi":"10.7155/jgaa.00642","DOIUrl":"https://doi.org/10.7155/jgaa.00642","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"159 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135450902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"$st$-Orientations with Few Transitive Edges","authors":"Carla Binucci, Walter Didimo, Maurizio Patrignani","doi":"10.7155/jgaa.00638","DOIUrl":"https://doi.org/10.7155/jgaa.00638","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"2016 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135450905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
. An important and well-studied problem in phylogenetics is to compute a consensus tree so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same set X of species. More recently, however, it has become of interest to find a consensus for a collection of more general, rooted directed acyclic graphs all of whose sink-sets are bijec-tively labeled by X , so called rooted phylogenetic networks . These networks are used to analyze the evolution of species that cross with one another, such as plants and viruses. In this paper, we introduce an algorithm for computing a consensus for a collection of so-called 1-nested phylogenetic networks. Our approach builds on a previous result by Rosell´o et al. that describes an encoding for any 1-nested phylogenetic network in terms of a collection of ordered pairs of subsets of X . More specifically, we characterize those collections of ordered pairs that arise as the encoding of some 1-nested phylogenetic network, and then use this characterization to compute a consensus network for a collection of t ≥ 1 1-nested networks in O ( t | X | 2 + | X | 3 ) time. Applying our algorithm to a collection of phylogenetic trees yields the well-known majority rule consensus tree. Our approach leads to several new directions for future work, and we expect that it should provide a useful new tool to help understand complex evolutionary scenarios.
． 系统发育学中一个重要且被广泛研究的问题是计算共识树，以总结一组有根系统发育树的共同特征，所有这些树的叶集都被相同的物种集X客观地标记。然而，最近，对于一组更一般的、有根的有向无环图的集合(所有这些图的汇集都被双客观地标记为X)，也就是所谓的有根系统发育网络，找到一个共识已经变得很有趣。这些网络被用来分析相互交叉的物种的进化，比如植物和病毒。在本文中，我们引入了一种算法，用于计算所谓的1套系统发育网络集合的一致性。我们的方法建立在Rosell ' o等人先前的结果的基础上，该结果描述了根据X的子集的有序对的集合对任何1嵌套系统发育网络的编码。更具体地说，我们描述了那些作为某种1嵌套系统发育网络编码而出现的有序对集合，然后使用该表征在O (t | X | 2 + | X | 3)时间内计算t≥11嵌套网络集合的共识网络。将我们的算法应用于系统发育树的集合产生了众所周知的多数规则共识树。我们的方法为未来的工作指明了几个新的方向，我们期望它能提供一个有用的新工具来帮助理解复杂的进化场景。
{"title":"Computing consensus networks for collections of 1-nested phylogenetic networks","authors":"K. Huber, V. Moulton, A. Spillner","doi":"10.7155/jgaa.00633","DOIUrl":"https://doi.org/10.7155/jgaa.00633","url":null,"abstract":". An important and well-studied problem in phylogenetics is to compute a consensus tree so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same set X of species. More recently, however, it has become of interest to find a consensus for a collection of more general, rooted directed acyclic graphs all of whose sink-sets are bijec-tively labeled by X , so called rooted phylogenetic networks . These networks are used to analyze the evolution of species that cross with one another, such as plants and viruses. In this paper, we introduce an algorithm for computing a consensus for a collection of so-called 1-nested phylogenetic networks. Our approach builds on a previous result by Rosell´o et al. that describes an encoding for any 1-nested phylogenetic network in terms of a collection of ordered pairs of subsets of X . More specifically, we characterize those collections of ordered pairs that arise as the encoding of some 1-nested phylogenetic network, and then use this characterization to compute a consensus network for a collection of t ≥ 1 1-nested networks in O ( t | X | 2 + | X | 3 ) time. Applying our algorithm to a collection of phylogenetic trees yields the well-known majority rule consensus tree. Our approach leads to several new directions for future work, and we expect that it should provide a useful new tool to help understand complex evolutionary scenarios.","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"1 1","pages":"541-563"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71225216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Let $G$ be a connected planar (but not yet embedded) graph and $F$ a set of additional edges not yet in $G$. The {multiple edge insertion} problem (MEI) asks for a drawing of $G+F$ with the minimum number of pairwise edge crossings, such that the subdrawing of $G$ is plane. An optimal solution to this problem approximates the crossing number of the graph $G+F$.
{"title":"Inserting Multiple Edges into a Planar Graph","authors":"Markus Chimani, Petr Hliněný","doi":"10.7155/jgaa.00631","DOIUrl":"https://doi.org/10.7155/jgaa.00631","url":null,"abstract":"Let $G$ be a connected planar (but not yet embedded) graph and $F$ a set of additional edges not yet in $G$. The {multiple edge insertion} problem (MEI) asks for a drawing of $G+F$ with the minimum number of pairwise edge crossings, such that the subdrawing of $G$ is plane. An optimal solution to this problem approximates the crossing number of the graph $G+F$. ","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"99 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135181353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Restricted rotation distance between k-ary trees","authors":"S. Cleary","doi":"10.7155/jgaa.00611","DOIUrl":"https://doi.org/10.7155/jgaa.00611","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"1 1","pages":"19-33"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71225093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Guest Editors' Foreword","authors":"Giordano Da Lozzo, P. Kindermann","doi":"10.7155/jgaa.00627","DOIUrl":"https://doi.org/10.7155/jgaa.00627","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71225343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Connected-closeness: A Visual Quantification of Distances in Network Layouts","authors":"Mathieu Jacomy","doi":"10.7155/jgaa.00626","DOIUrl":"https://doi.org/10.7155/jgaa.00626","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"1 1","pages":"341-404"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71225330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Walter Didimo, Michael Kaufmann, Giuseppe Liotta, Giacomo Ortali
{"title":"Rectilinear Planarity of Partial 2-Trees","authors":"Walter Didimo, Michael Kaufmann, Giuseppe Liotta, Giacomo Ortali","doi":"10.7155/jgaa.00640","DOIUrl":"https://doi.org/10.7155/jgaa.00640","url":null,"abstract":"","PeriodicalId":35667,"journal":{"name":"Journal of Graph Algorithms and Applications","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135450477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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