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Search results for: phylogenetic tree metrics
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Analyzing sets of phylogenetic trees using metrics
PublicationThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationships between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations among organisms and geographical areas. In this paper, we describe a general method for comparing phylogenetictrees...
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Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages
PublicationThe ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One...
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Critical Case Stochastic Phylogenetic Tree Model via the Laplace Transform
PublicationBirth–and–death models are now a common mathematical tool to describe branching patterns observed in real–world phylogenetic trees. Liggett and Schinazi (2009) is one such example. The authors propose a simple birth–and–death model that is compatible with phylogenetic trees of both influenza and HIV, depending on the birth rate parameter. An interesting special case of this model is the critical case where the birth rate equals the...
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Analyzing sets of phylogenetic trees obtained from bayesian MCMC process using topology metrics
PublicationThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationship between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations amongorganisms and geographical areas.In the paper, we describe a general method for comparing hylogenetic trees....
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Comparing phylogenetic trees using a minimum weight perfect matching
PublicationA phylogenetic tree represents historical evolutionary relationshipbetween different species or organisms. There are various methods for reconstructing phylogenetic trees.Applying those techniques usually results in different treesfor the same input data. An important problem is to determinehow distant two trees reconstructed in such a wayare from each other. Comparing phylogenetic trees is alsouseful in mining phylogenetic information...
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Visual TreeCmp : Comprehensive Comparison of Phylogenetic Trees on the Web
Publication1. We present Visual TreeCmp—a package of applications for comparing phylogenetic tree sets. 2. Visual TreeCmp includes a graphical web interface allowing the visualization of compared trees and command line application extended by comparison methods recently proposed in the literature. 3. The phylogenetic tree similarity analysis in Visual TreeCmp can be performed using eighteen metrics, of which 11 are dedicated to rooted trees...
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Comparing Arbitrary Unrooted Phylogenetic Trees Using Generalized Matching Split Distance
PublicationIn the paper, we describe a method for comparing arbitrary, not necessary fully resolved, unrooted phylogenetic trees. Proposed method is based on finding a minimum weight matching in bipartite graphs and can be regarded as a generalization of well-known Robinson-Foulds distance. We present some properties and advantages of the new distance. We also investigate some properties of presented distance in a common biological problem...
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Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions
PublicationAbility to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in...
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Phylogenetic analysis of Oncidieae subtribe - matK plastid region
Open Research DataThe dataset contains alignment and consensus matrix files, and results of phylogenetic analysis of plastid matK region from 186 orchid species considered to belong Oncidieae subtribe. Sequences were assessed from NCBI GeneBank (list of all records with identifiers in the separate file)
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Phylogenetic analysis of Oncidieae subtribe - ITS1-5,8S-ITS2
Open Research DataThe dataset contains alignment and consensus matrix files, and results of phylogenetic analysis of ITS1- 5,8S-ITS2 region from 186 orchid species considered to belong Oncidieae subtribe. Sequences were assessed from NCBI GeneBank (list of all records with identifiers in the separate file)
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Psychological and physical components in forming preferences on urban greenery management – The case of trees
PublicationPublic opinion is increasingly important in managing urban greenery. In this regard, this study demonstrates the importance of sociological (environmental worldviews), psychological (place attachment, perceived benefits of trees), and physical factors (type of building people live in, and urban greenery) in forming residents’ opinions on whether the municipality or landowners should decide about tree removal on private land. Logistic...
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Intra-operative biopsy in chronic sinusitis detects pathogenic Escherichia coli that carry fimG/H, fyuA and agn43 genes coding biofilm formation
PublicationThe aim of this study was to investigate whether or not surgical biopsy of sinus tissue in chronic sinusitis, not responsive to treatment, would detect E. coli. We intended to evaluate E. coli virulence genes, therefore dispute the causal role of such an unusual microorganism in chronic sinusitis, as well as consider effective pathogen-targeted therapy. Patients with E. coli isolated by intra-operative puncture biopsy were included...
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Metrics for green analytical chemistry
PublicationGreen analytical chemistry, although not being a new concept, does not have a greenness metrics system. Green chemistry metrics are not suitable for analytical procedure assessment because they often refer to the mass of the product. Some efforts have been made to develop suitable metrics for analytical chemistry. Some are simple to use but do not cover all aspects of analytical methods’ environmental impact. Others are more comprehensive...
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Green analytical chemistry metrics: A review
PublicationGreen analytical chemistry encourages reducing the use of toxic chemicals/reagents, using energy-efficient equipment, and generating minimal waste. The recent trends in analytical method development focus on the miniaturization of the sample preparation devices, the development of solventless or solvent-minimized extraction techniques, and the utilization of less toxic solvents. The twelve principles of GAC serve as a basic guideline...
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Construction of phylogenetic trees with topological constraints
PublicationThis paper proposes a method of reconstruction of phylogenetic trees based on heuristic search with topological constraints. Using topological constraints it is possible to reduce the set of solutions as well as to enforce that the result is consistent with a given hypothesis about the evolution process within some group of species. Along with this work a number of algorithms used for phylogenetic analysis were implemented. Those...
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The complexity of bicriteria tree-depth
PublicationThe tree-depth problem can be seen as finding an elimination tree of minimum height for a given input graph G. We introduce a bicriteria generalization in which additionally the width of the elimination tree needs to be bounded by some input integer b. We are interested in the case when G is the line graph of a tree, proving that the problem is NP-hard and obtaining a polynomial-time additive 2b-approximation algorithm. This particular...
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Polynomial triset metric for unrooted phylogenetic trees
Publicationthe following paper presents a polynomial triset metric for unrooted phylogenetic trees (based on weighted bipartite graphs and the method of determining a minimum edge cover) and its basic characteristics. also a list of further directions of research and examples of the wider use of this metric is presented.
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Aiming at methods’ wider adoption: Applicability determinants and metrics
PublicationNumerous computer science methods and techniques have been proposed by the scientific community. However, depending on the domain, only their minor fraction has met wider adoption. This paper brings attention to the concept of applicability - the notion that is well acknowledged in the scientific field but have not been analysed with respect to determinants, metrics and systematisation. The primary objective of the study was to...
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Green Chemistry Metrics with Special Reference to Green Analytical Chemistry
PublicationThe concept of green chemistry is widely recognized in chemical laboratories. To properly measure an environmental impact of chemical processes, dedicated assessment tools are required. This paper summarizes the current state of knowledge in the field of development of green chemistry and green analytical chemistry metrics. The diverse methods used for evaluation of the greenness of organic synthesis, such as eco-footprint, E-Factor,...
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On extremal sizes of locally k-tree graphs
PublicationA graph G is a locally k-tree graph if for any vertex v the subgraph induced by the neighbours of v is a k-tree, k>=0, where 0-tree is an edgeless graph, 1-tree is a tree. We characterize the minimum-size locally k-trees with n vertices. The minimum-size connected locally k-trees are simply (k + 1)-trees. For k >= 1, we construct locally k-trees which are maximal with respect to the spanning subgraph relation. Consequently, the...