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24
On Nakhleh's metric for reduced phylogenetic networks
 IEEE/ACM Transactions on Computational Biology and Bioinformatics
, 2009
"... Abstract—We prove that Nakhleh’s metric for reduced phylogenetic networks is also a metric on the classes of treechild phylogenetic networks, semibinary treesibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogene ..."
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Abstract—We prove that Nakhleh’s metric for reduced phylogenetic networks is also a metric on the classes of treechild phylogenetic networks, semibinary treesibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phylogenetic networks. Index Terms—Biology and genetics, graph algorithms, network problems. Ç 1
PROTEIN DOMAIN PHYLOGENIES Information Theory and Evolutionary Dynamics
"... information theory; JensenShannon divergence; evolutionary dynamics; phylogenetic trees; SUPFAM The everincreasing wealth of wholegenome information prompts for phylogenies based on entire genomes. The quest for a good distance measure, however, poses a big challenge; e.g. because of largescale ..."
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information theory; JensenShannon divergence; evolutionary dynamics; phylogenetic trees; SUPFAM The everincreasing wealth of wholegenome information prompts for phylogenies based on entire genomes. The quest for a good distance measure, however, poses a big challenge; e.g. because of largescale evolutionary events such as genomic rearrangements or inversions. We introduce here an information theory driven measure that for the encoded protein domain composition of genomes as protein domains are key evolutionary entities. Thus the new method focuses on selective advantageous events. As evolving different protein domain compositions is more complex than single point mutations, the method makes longer evolutionary times accessible. Illustrating the new methodology we extract several phylogenetic trees for some 700 genomes, e.g. the separation of the three kingdoms of life, trees for mammals and bacillales, and a speculative result for plants (monocotyledons and dicotyledons). The method itself is shown to be robust against incomplete genome sampling. It has a consistent interpretation in both, information space at the sequence/information level and at the level of stochastic, evolutionary dynamics. In contrast to established protocols it becomes more accurate as more organisms are taken into account. Finally we show the equivalence to a (simplified) model of evolutionary dynamics of proteomes. 1
QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS
, 2012
"... Accepted (Day Month Year) Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogen ..."
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Accepted (Day Month Year) Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analogue of levelk networks. In particular, we give an equivalence theorem between circular split systems and unrooted level1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted levelk phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.
G.: On Nakhleh’s latest metric for phylogenetic networks
 IEEE/ACM Transactions on Computational Biology and Bioinformatics
, 2009
"... Abstract. We prove that Nakhleh’s latest ‘metric ’ for phylogenetic networks is a metric on the classes of treechild phylogenetic networks, of semibinary time consistent treesibling phylogenetic networks, and of multilabeled phylogenetic trees.We also prove that it separates distinguishable phyl ..."
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Abstract. We prove that Nakhleh’s latest ‘metric ’ for phylogenetic networks is a metric on the classes of treechild phylogenetic networks, of semibinary time consistent treesibling phylogenetic networks, and of multilabeled phylogenetic trees.We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. 1
constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints
, 2009
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METHODOLOGY ARTICLE Open Access The performance of the Congruence Among
"... Background: CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tes ..."
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Background: CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions. Results: Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices. Conclusions: Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously. Background
The Diverse Applications of Cladistic Analysis of Molecular Evolution, with Special Reference to Nested Clade Analysis
, 2010
"... Abstract: The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many w ..."
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Abstract: The genetic variation found in small regions of the genomes of many species can be arranged into haplotype trees that reflect the evolutionary genealogy of the DNA lineages found in that region and the accumulation of mutations on those lineages. This review demonstrates some of the many ways in which clades (branches) of haplotype trees have been applied in recent years, including the study of genotype/phenotype associations at candidate loci and in genomewide association studies, the phylogeographic history of species, human evolution, the conservation of endangered species, and the identification of species.
Telling the Whole Story in a 10,000Genome World
"... Background: Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct trees of microbial life: such trees are easily interpreted and allow ..."
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Background: Genome sequencing has revolutionized our view of the relationships among genomes, particularly in revealing the confounding effects of lateral genetic transfer (LGT). Phylogenomic techniques have been used to construct trees of microbial life: such trees are easily interpreted and allow the use of a subset of genomes as 'proxies ' for the full set. However, LGT impacts on the positioning of taxonomic groups in genome trees, and complicates our efforts to assess the degree to which different organisms are related. Network and graph approaches can reveal complex sets of relationships, but applying these techniques to large data sets is a significant challenge. Notwithstanding the question of what exactly it might represent, generating and interpreting a Tree of All Genomes or Network of All Genomes that parallels the widely used smallsubunit ribosomal DNA tree will only be feasible if current algorithms can be improved. Results: The rate at which new taxonomic groups and novel protein sequences are accumulating, and the complex relationships among even the mostsimilar genomes, show that homology and proxybased approaches to simplifying large sets of genomes will be necessary but not sufficient to solve the analysis problem. A phylogenomic analysis of 1173 sequenced bacterial and