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Search results for: computer phylogenetics
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MOLECULAR PHYLOGENETICS AND EVOLUTION
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LECTURE NOTES IN COMPUTER SCIENCE
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Procedia Computer Science
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THEORETICAL COMPUTER SCIENCE
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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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Properties of the triset metric for phylogenetic trees
Publicationthe following paper presents a new polynomial time metric for unrootedphylogenetic trees (based on weighted bipartite graphs and the method ofdetermining a minimum perfect matching) and its properties. also many its properties are presented.
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Communications in Computer and Information Science
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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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Phylogenetic Placement and Taxonomy of the Genus Hederorkis (Orchidaceae)
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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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On a matching distance between rooted phylogenetic trees
PublicationThe Robinson–Foulds (RF) distance is the most popular method of evaluating the dissimilarity between phylogenetic trees. In this paper, we define and explore in detail properties of the Matching Cluster (MC) distance, which can be regarded as a refinement of the RF metric for rooted trees. Similarly to RF, MC operates on clusters of compared trees, but the distance evaluation is more complex. Using the graph theoretic approach...
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
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Matching Split Distance for Unrooted Binary Phylogenetic Trees
PublicationRekonstrukcja drzew ewolucji jest jednym z głównych celów w bioinformatyce. Drzewa filogenetyczne reprezentuje historię ewolucji i związki pokrewieństwa między różnymi gatunkami. W pracy proponujemy nową ogólną metodę określania odległości między nieukorzenionymi drzewami filogenetycznymi, szczególnie użyteczną dla dużych zbiorów gatunków. Następnie podajemy szczegółowe własności jednej metryki określonej przy użyciu tej metody...
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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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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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Computer synchronization of power generators
PublicationAktualną staje się kwestia opracowania odpowiednich algorytmów pomiarów i obliczeń, według których będzie możliwe prowadzenie procesu automatycznej synchronizacji bezpośrednio z wykorzystaniem komputera. W artykule przedstawiono komputerową metodę realizacji warunku fazowego podczas synchronizacji oraz podano wyniki jej badań symulacyjnych oraz badań na obiektach rzeczywistych.
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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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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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Palicella, a new genus of lichenized fungi and its phylogenetic position withinLecanoraceae
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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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Gesture-based computer control system
PublicationIn the paper a system for controlling computer applications by hand gestures is presented. First, selected methods used for gesture recognition are described. The system hardware and a way of controlling a computer by gestures are described. The architecture of the software along with hand gesture recognition methods and algorithms used are presented. Examples of basic and complex gestures recognized by the system are given.
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Computer application for railway track realignment
PublicationThe topic of this article is the issue of railway track realignment. For this purpose, a computer software application was created that supports computations and generates a report needed for regulation of the trajectory of the railway. This program gives the ability to import data from measurement of the railway trajectory and then perform the calculation of the mathematical realignment. The result of this calculation is the basis...
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Software Agents for Computer Network Security
PublicationThe chapter presents applications of multi-agent technology for design and implementation of agent-based systems intended to cooperatively solve several critical tasks in the area of computer network security. These systems are Agent-based Generator of Computer Attacks (AGCA), Multi-agent Intrusion Detection and Protection System (MIDPS), Agent-based Environment for Simulation of DDoS Attacks and Defense (AESAD) and Mobile Agent...
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Applications of Computer Vision in Automation and Robotics
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Erosion of privacy in computer vision systems
PublicationW pracy przedstawiono problemy, które mogą wystąpić, gdy technologia komputerowego wzroku zostanie zaimplementowana w urządzeniach wykorzystywanych w codziennym życiu. Przeprowadzono także dyskusję socjologicznych konsekwencji stosowania biometrii, automatycznego śledzenia ruchu i interpretacji obrazu. Omówiono też problemy wynikające z połączenia komputerowego wzroku z możliwościami oferowanymi przez Internet.
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Computer modeling and testing of structural metamaterials
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Industrial computer networks and functional safety
PublicationW rozdziale monografii przedstawiono wybrane aspekty bezpieczeństwa funkcjonalnego na przykładzie przemysłowych sieci komputerowych stosowanych w obiektach infrastruktury krytycznej. Pierwszą cześć rozdziału poświęcono omówieniu klasycznych rozwiązań w zakresie sieci komputerowych. Drugą część rozdziału stanowi analiza przypadku typowej przemysłowej sieci komputerowej z uwzględnieniem aspektów bezpieczeństwa funkcjonalnego.
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Computer-aided Measurements of Turbine Blades
PublicationPrzedstawiono skomputeryzowane pomiary profili łopatek turbinowych po szlifowaniu. W pracy wykorzystano program komputerowy, który może być zastosowany bezpośrednio przez operatora obrabiarki, opracowany na bazie Microsoft Excel.
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Cost assessment of computer security activities
PublicationComprehensive cost-benefit analysis plays a crucial role in the decision-making process when it comes to investments in information security solutions. The cost of breaches needs to be analysed in the context of spending on protection measures. However, no methods exist that facilitate the quick and rough prediction of true expenditures on security protection systems. Rafal Leszczyna of Gdansk University of Technology presents...
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Computer aided funcional safety assessment
PublicationReferat porusza wybrane zagadnienia związane z oceną bezpieczeństwa funkcjonalnego w nawiązaniu do normy międzynarodowej IEC 61508. Podkreśla się znaczenie modelowania probabilistycznego systemów elektrycznych, elektronicznych i programowalnych elektronicznych (E/E/PE). Opisuje się wyznaczanie poziomu nienaruszalności bezpieczeństwa (SIL). W następnym kroku analizy weryfikuje się poziom SIL w procesie modelowania probabilistycznego...
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Computers and Concrete
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COMPUTERS & STRUCTURES
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COMPUTER
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Wygnij swój komputer.
PublicationW artykule przedstawiono wspolczesne trendy w rozwoju interfejsów uzytkownika wybranych rozwiazan infomatycznych.
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Interakcja człowiek-komputer
PublicationKsiążka omawia najważniejsze zagadnienia kształtowania interakcji człowiek-komputer, występujące podczas projektowania produktu informatycznego. Tematyka książki obejmuje metody stosowane kolejno podczas określania wymagań, projektowania, testowania i oceny rozwiązań interfejsu użytkownika. Przyjęty sposób prezentacji materiału ma na celu również podkreślenie, że wysoka jakość użytkowa produktu informatycznego nie wynika wyłącznie...
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Komputer w labiryncie
PublicationProgramiści piszą programy, które potrafią robić wiele różnych rzeczy: odtwarzać filmy, prognozować pogodę, pomagać w nauce języków obcych czy matematyki. Ale czy wiesz, że można zaprogramować komputer tak, aby tworzył labirynty? W dodatku takie, które zawierają tajne informacje!
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Phylogenetics and phylogeography of red deer mtDNA lineages during the last 50 000 years in Eurasia
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COMPUTER PHYSICS COMMUNICATIONS
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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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Morphologic, Phylogenetic and Chemical Characterization of a Brackish Colonial Picocyanobacterium (Coelosphaeriaceae) with Bioactive Properties
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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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Journal of Applied Computer Science
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COMPUTER ANALYSIS OF HYDRAULIC CONDITIONS IN A SANITARY CHAMBER
PublicationThis paper presents analysis of hydraulic conditions of sewage flow down the slipway (ramp) in the collecting sanitary chamber connecting 3 collectors on the inlet: ⌀600, ⌀800 and ⌀1400 and one on the outlet ⌀1600 mm, with a maximum difference of elevation 5 m. The mathematical model has been made and hydraulic calculations were carried out in steady flow conditions. Then wastewater surface elevation, energy grade line elevation,...
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Generalized access control in hierarchical computer network
PublicationThe paper presents the design of the security layer for a distributed system located in the multizone hierarchical computer network. Depending on the zone from which a client’s request comes to the system and the type of the request, it will be either authorized or rejected. There is one common layer for the access to all the business services and interactions between them. Unlike the commonly used RBAC model, this system enforces...
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Utilization of fuzzy rules in computer character animation
PublicationThe chapter presents a method for automatic enhancement of computer character animation utilizing fuzzy inference. First the user designs a prototype version of animation, with keyframes only for important poses, roughly describing the action. Then animation is enriched with new motion phases calculated by the fuzzy inference system using descriptors given by the user. Various degrees of motion fluency and naturalness are possible...
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Modelling and computer animation of geodetic field work
Publication3D modelling of objects is a way of obtaining information, while the visualization of geospatial data is becoming a production task in the scope of surveying. Visualization of geospatial data provides effective tools for analysis information about the land surface, land cover, its features, properties etc. Computer animations, both 2D images and 3D are becoming additional, expected and clear form for presentation results of geodetic...
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Displacements of chimney in the light of computer calculations and surveying
PublicationThe article presents the numerical analysis of reinforced concrete chimney displacements, which was carried out geodetic measurements.
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Computer analysis of multiple-choice examination documents
PublicationOpisany system AATE wyposażony jest w edytor testów, za pomocą którego egzaminator przygotowuje test egzaminacyjny. Utworzony test ze swoimi parametrami jest pamiętany w bazie danych i następnie może być wydrukowany. Po przeprowadzeniu egzaminu wypełnione formularze za pomocą skanera z podajnikiem wprowadza się do komputera. W komputerze system analizuje formularze i odczytane odpowiedzi porównuje się z wzorcami przechowywanymi...
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Computer Aided Telediagnostics System for Stoma Patients
PublicationStoma surgery may concern patients with colorectal cancer and inflammatory bowel disease. More than half of patients diagnosed with colon cancer present at an advanced stage, and palliative treatment may involve stoma formation. This type of surgery may change the patient’s life strongly, therefore they should receive special medical care. The paper presents the assumptions, concept, and architecture of the Stoma-Alert diagnosis...
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Computer Aided Design of Wood Pellet Machines
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