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INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS
2005
Proceedings of the 3rd Asia-Pacific Bioinformatics Conference
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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
2006
Journal of Bioinformatics and Computational Biology
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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
2008
IEEE/ACM Transactions on Computational Biology & Bioinformatics
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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]
2015
arXiv
pre-print
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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
2019
Algorithms
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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
2015
Philosophical Transactions of the Royal Society of London. Biological Sciences
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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
2018
Bioinformatics
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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]
2018
bioRxiv
pre-print
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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]
2010
Hybrid Optimization
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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
2000
Molecular Phylogenetics and Evolution
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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]
2020
arXiv
pre-print
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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]
2008
Msphere
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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
2007
Computer journal
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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
2013
Algorithms for Molecular Biology
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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
2019
Journal of Graph Algorithms and Applications
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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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