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INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

YING-JUN HE, TRINH N.D. HUYNH, JESPER JANSSON, WING-KIN SUNG
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set T and none of the rooted triplets in another given  ...  However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly  ...  Introduction The evolutionary relationships among a set of species S are commonly described by a phylogenetic tree or a phylogenetic network.  ... 
doi:10.1142/9781860947322_0034 fatcat:x5uatupgobaipmbg5l53hmjwp4

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

YING-JUN HE, TRINH N. D. HUYNH, JESPER JANSSON, WING-KIN SUNG
2006 Journal of Bioinformatics and Computational Biology  
In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set T and none of the rooted triplets in another given  ...  However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly  ...  Introduction The evolutionary relationships among a set of species S are commonly described by a phylogenetic tree or a phylogenetic network.  ... 
doi:10.1142/s0219720006001709 pmid:16568542 fatcat:criaznxumvctvp25olit6ugk5u

The Undirected Incomplete Perfect Phylogeny Problem

R.V. Satya, A. Mukherjee
2008 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, we deal with the unrestricted version of the problem, where the root of the phylogeny is neither available nor trivially recoverable from the data.  ...  The earlier approaches for both these problems dealt with restricted versions of the problem, where the root is either available or can be trivially reconstructed from the data, or certain assumptions  ...  In a perfect phylogeny, there are certain relationships between the forbidden pairs of three columns.  ... 
doi:10.1109/tcbb.2007.70218 pmid:18989047 fatcat:wc2p26idcrgmrgf2odfscfhnqq

Genome-scale phylogenetic analysis finds extensive gene transfer among Fungi [article]

Gergely J. Szöllősi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin, Bastien Boussau
2015 arXiv   pre-print
Ancestral genomes are inferred in both clades using two types of methods.  ...  We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences.  ...  In short, this means that gene transfers are forbidden.  ... 
arXiv:1505.06067v2 fatcat:be2culb4i5cohojqooxavflc54

Parameterized Algorithms in Bioinformatics: An Overview

Laurent Bulteau, Mathias Weller
2019 Algorithms  
We cover sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics.  ...  ROOTED TRIPLET INCONSISTENCY (RTI) Results.  ...  A (rooted) phylogenetic tree is a (rooted) phylogenetic network whose underlying undirected graph is acyclic.  ... 
doi:10.3390/a12120256 fatcat:4dhjdnpibzh43iifgan2fu6bwa

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

Gergely J. Szöllősi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin, Bastien Boussau
2015 Philosophical Transactions of the Royal Society of London. Biological Sciences  
In short, this means that gene transfers are forbidden.  ...  Owing to this design, families present only in two Ascomycota have been discarded from our dataset, and therefore cannot be inferred at the root.  ... 
doi:10.1098/rstb.2014.0335 pmid:26323765 pmcid:PMC4571573 fatcat:phqwcxzozjcydhzkyuuoiolrmm

Accurate prediction of orthologs in the presence of divergence after duplication

Manuel Lafond, Mona Meghdari Miardan, David Sankoff
2018 Bioinformatics  
Results: We formalize the notion of divergence after duplication and provide a theoretical basis for the inference of primary and secondary orthologs.  ...  This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function.  ...  On the other hand, phylogeny-based methods do not attempt in the first instance to group genes together but rather aim to identify orthologs by inferring the lowest common ancestor (lca) relationships  ... 
doi:10.1093/bioinformatics/bty242 pmid:29950018 pmcid:PMC6022570 fatcat:abs2qab4rjcetbmiwnffm6w4py

Accurate prediction of orthologs in the presence of divergence after duplication [article]

Manuel Lafond, Mona Meghdari Miardan, David Sankoff
2018 bioRxiv   pre-print
Results: We formalize the notion of divergence after duplication, and provide a theoretical basis for the inference of primary and secondary orthologs.  ...  This has important consequences on the prediction of orthology relationships, since two orthologous genes separated by divergence after duplication may differ in both sequence and function.  ...  by phylogenetic methods.  ... 
doi:10.1101/294405 fatcat:6f7oezawjzbjbdl3esjvirz7f4

Bioinformatics: A Challenge to Constraint Programming [chapter]

Pedro Barahona, Ludwig Krippahl, Olivier Perriquet
2010 Hybrid Optimization  
One example is to use a fundamental property of rooted phylogenetic trees.  ...  Phylogenetic trees, which represent the evolutionary relationships between taxonomic groups, are often calculated from gene or protein sequences.  ... 
doi:10.1007/978-1-4419-1644-0_14 fatcat:wpukgksb45da3i2ctaxhdgn6ya

Median Networks: Speedy Construction and Greedy Reduction, One Simulation, and Two Case Studies from Human mtDNA

Hans-Jürgen Bandelt, Vincent Macaulay, Martin Richards
2000 Molecular Phylogenetics and Evolution  
Molecular data sets characterized by few phylogenetically informative characters with a broad spectrum of mutation rates, such as intraspecific controlregion sequence variation of human mitochondrial DNA  ...  A coalescent simulation tailored to human mtDNA variation in Eurasia testifies to the usefulness of reduced median networks, while highlighting notorious problems faced by all phylogenetic methods in this  ...  The character states of the branching nodes in the tree constructed from a clique can be inferred from suitably chosen triplets of sampled haplotypes in median fashion-that is to say, by taking the majority  ... 
doi:10.1006/mpev.2000.0792 pmid:10877936 fatcat:zbfrkjj7l5f6nl2uktxsjpkwte

Complexity of modification problems for best match graphs [article]

David Schaller, Peter F. Stadler, Marc Hellmuth
2020 arXiv   pre-print
Best match graphs (BMGs) are vertex-colored directed graphs that were introduced to model the relationships of genes (vertices) from different species (colors) given an underlying evolutionary tree that  ...  To this end, we provide a novel characterization of BMGs in terms of triples (binary trees on three leaves) and a characterization of BMGs with two colors in terms of forbidden subgraphs.  ...  A phylogenetic tree T (on L) is an (undirected) rooted tree with root ρ T , leaf set L = L(T ) ⊆ V (T ) and inner vertices V 0 (T ) = V (T ) \ L such that each inner vertex of T (except possibly the root  ... 
arXiv:2006.16909v3 fatcat:opqvptidn5eu3bxou6hfoy6tma

Fixed-Parameter Algorithms in Phylogenetics [chapter]

Jens Gramm, Arfst Nickelsen, Till Tantau
2008 Msphere  
We survey the use of fixed-parameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships.  ...  The central problem in phylogenetics is the reconstruction of the evolutionary history of biological species, but its methods also apply to linguistics, philology, or architecture.  ...  (Note that a set of quartets that share a common taxon can be thought of as a set of directed triplets.)  ... 
doi:10.1007/978-1-60327-159-2_24 pmid:18566780 fatcat:b7iiquxu5bcmxf776g4crrnepi

Fixed-Parameter Algorithms in Phylogenetics

J. Gramm, A. Nickelsen, T. Tantau
2007 Computer journal  
We survey the use of fixed-parameter algorithms in the field of phylogenetics, which is the study of evolutionary relationships.  ...  The central problem in phylogenetics is the reconstruction of the evolutionary history of biological species, but its methods also apply to linguistics, philology, or architecture.  ...  (Note that a set of quartets that share a common taxon can be thought of as a set of directed triplets.)  ... 
doi:10.1093/comjnl/bxm049 fatcat:txfzhsnt3zebffedefjbfacwue

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

Daniele Catanzaro, Ramamoorthi Ravi, Russell Schwartz
2013 Algorithms for Molecular Biology  
The literature on molecular phylogenetics proposes a number of criteria for selecting a phylogeny from among plausible alternatives.  ...  http://www.almob.org/content/8/1/3 Background Molecular phylogenetics studies the hierarchical evolutionary relationships among species, or taxa, by means of molecular data such as DNA, RNA, amino acid  ...  For example, the use of molecular phylogenetics was of considerable assistance in predicting the evolution of human influenza A [4] , understanding the relationships between the virulence and the genetic  ... 
doi:10.1186/1748-7188-8-3 pmid:23343437 pmcid:PMC3599976 fatcat:xnw5qygkcvbinggud2obpnplqi

Treewidth of display graphs: bounds, brambles and applications

Remie Janssen, Mark Jones, Steven Kelk, Georgios Stamoulis, Taoyang Wu
2019 Journal of Graph Algorithms and Applications  
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks.  ...  Next we show that if a phylogenetic network displays (i.e. topologically embeds) a phylogenetic tree, the treewidth of their display graph is bounded by a function of the treewidth of the original network  ...  This is not an onerous restriction, since many phylogenetic inference methods construct unrooted, binary trees. We refer the reader to [41, 18] for further background on phylogenetics.  ... 
doi:10.7155/jgaa.00508 fatcat:hy7gfl4umjbm7pxx2ojwwfofla
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