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Dissertations / Theses on the topic 'Phylogenetic tree'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Yu, Junjie, and 于俊杰. "Phylogenetic tree reconstruction with protein linkage." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49618167.

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Phylogenetic tree reconstruction for a set of species is an important problem for understanding the evolutionary history of the species. Existing algorithms usually represent each species as a binary string with each bit indicating whether a particular gene/protein exists in the species. Given the topology of a phylogenetic tree with each leaf representing a species (a binary string of equal length) and each internal node representing the hypothetical ancestor, the Fitch-Hartigan algorithm and the Sankoff algorithm are two polynomial-time algorithms which assign binary strings to internal nod

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2

Bansal, Mukul Subodh. "Algorithms for efficient phylogenetic tree construction." [Ames, Iowa : Iowa State University], 2009.

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3

Jirásková, Kristýna. "Metody rekonstrukce fylogenetických superstromů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219518.

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The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.

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Kosíř, Kamil. "Metody rekonstrukce fylogenetických superstromů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-220860.

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The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.

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5

Candy, Robin. "Ordinal and convex assumptions in phylogenetic tree reconstruction." Thesis, University of Canterbury. School of Mathematics and Statistics, 2014. http://hdl.handle.net/10092/9594.

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Phylogenetics is a field primarily concerned with the reconstruction of the evolutionary history of present day species. Evolutionary history is often modeled by a phylogenetic tree, similar to a family tree. To recreate a phylogenetic tree from information about current species, one needs to make assumptions about the evolutionary process. These assumptions can range from full parametrised models of evolution to simple observations. This thesis looks at the reconstruction of phylogenetic trees under two different assumptions. The first, known as the ordinal assumption, has been previously stu

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6

Dees, Jonathan Andrew. "Effects of Phylogenetic Tree Style on Student Comprehension." Diss., North Dakota State University, 2017. https://hdl.handle.net/10365/26496.

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Phylogenetic trees are powerful tools of evolutionary biology that have become prominent across the life sciences. Consequently, learning to interpret and reason from phylogenetic trees is now an essential component of biology education. However, students often struggle to understand these diagrams, even after explicit instruction. One factor that has been observed to affect student understanding of phylogenetic trees is style (i.e., diagonal or bracket). The goal of this dissertation research was to systematically explore effects of style on student interpretations and construction of phyloge

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7

Li, Shuying. "Phylogenetic tree construction using markov chain monte carlo /." The Ohio State University, 1996. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487942182323916.

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8

Arvestad, Isaac, and Henrik Lagebrand. "Implementing Bayesian phylogenetic tree inference with Sequential Monte Carlo and the Phylogenetic Likelihood Library." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-229429.

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We investigate the usability of the Phylogenetic Likelihood Library (PLL) in Bayesian phylogenetic tree inference using Sequential Monte Carlo (SMC) algorithms. This is done by implementing two different versions of the same algorithm with two different approaches of the use of PLL. The implementation using the main PLL API encountered performance issues that the lower level implementation did not. We conclude that it is possible to use PLL in SMC methods but it is unclear if the main API is suitable.<br>Vi undersöker om programspråksbiblioteket Phylogenetic Likelihood Library (PLL) kan använd

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9

de, Jong Jamie Victoria. "Neighbourhoods of Phylogenetic Trees: Exact and Asymptotic Counts." Thesis, University of Canterbury. Mathematics and Statistics, 2015. http://hdl.handle.net/10092/10435.

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A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for the reconstruction of trees, it is crucial to understand the size and structure of neighbourhoods of trees under tree rearrangement operations. The diameter and size of the immediate neighbourhood of a tree has been well-studied, however little is known about the number of trees at distance two, three or (more generally) k from a given tree. In this thesis we explore previous results on the size of these neighbourhoods under common tree

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10

Sundberg, Kenneth A. "Partition Based Phylogenetic Search." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2583.

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Evolutionary relationships are key to modern understanding of biological systems. Phylogenetic search is the means by which these relationships are inferred. Phylogenetic search is NP-Hard. As such it is necessary to employ heuristic methods. This work proposes new methods based on viewing the relationships between species as sets of partitions. These methods produce more parsimonious phylogenies than current methods.

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11

Wang, Qiang. "Maximum likelihood estimation of phylogenetic tree with evolutionary parameters." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1083177084.

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Thesis (Ph. D.)--Ohio State University, 2004.<br>Title from first page of PDF file. Document formatted into pages; contains xi, 167 p.; also includes graphics Includes bibliographical references (p. 157-167). Available online via OhioLINK's ETD Center

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12

Zhu, Sha (Joe). "Stochastic tree models and probabilistic modelling of gene trees of given species networks." Thesis, University of Canterbury. Department of Mathematics and Statistics, 2013. http://hdl.handle.net/10092/7944.

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In the pre-genomic era, the relationships among species and their evolutionary histories were often determined by examining the fossil records. In the genomic era, these relationships are identified by analysing the genetic data, which also enables us to take a close-up view of the differences between the individual samples. Nevertheless, these relationships are often described by a tree-like structure or a network. In this thesis, we investigate some of the models that are used to describe these relationships. This thesis can be divided into two main parts. The first part focuses on investig

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Wang, Jingjing. "A PARALLEL APPROACH TO MULTIPLE SEQUENCES ALIGNMENT AND PHYLOGENETIC TREE LABELING." OpenSIUC, 2010. https://opensiuc.lib.siu.edu/theses/246.

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An evolutionary tree represents the relationship among a group of species, DNA or protein sequences, and play fundamental roles in biological lineage research. A high quality tree construction relies heavily on optimal multiple sequence alignment (MSA), which aligns three or more sequence simultaneously to derive the similarity. On the other hand, a good tree can also be used to guide the MSA process. Due to the high computational cost to conduct both the MSA and tree construction, parallel approaches are exploited to utilize the enormous amount of computing power and memory housed in a superc

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14

Tian, Yuan. "Topics in Phylogenetic Species Tree Inference under the Coalescent Model." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480422907698897.

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15

Honorio, Coronado Euridice Nora. "Phylogeography and phylogenetic diversity of Amazon tree species and communities." Thesis, University of Leeds, 2013. http://etheses.whiterose.ac.uk/4605/.

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The Amazon rain forest is the most diverse ecosystem on Earth, harbouring more than ten thousand tree species. In this project, I used ecological and molecular information to explore how ecological factors and historical events have determined the species distributions and population genetic structure of tree species and the phylogenetic diversity of tree communities in the Amazon rain forest. Chapter 2 indicates that seasonally dry vegetation in northern South America represents a barrier to migration for Ficus insipida (Moraceae) and other wet-adapted Amazonian tree species as they have diff

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Kalaghatgi, Prabhav [Verfasser]. "Inferring phylogenetic trees under the general Markov model via a minimum spanning tree backbone / Prabhav Kalaghatgi." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2020. http://d-nb.info/1218075465/34.

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17

Cheon, Sooyoung. "Protein folding and phylogenetic tree reconstruction using stochastic approximation Monte Carlo." Texas A&M University, 2003. http://hdl.handle.net/1969.1/5785.

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Recently, the stochastic approximation Monte Carlo algorithm has been proposed by Liang et al. (2005) as a general-purpose stochastic optimization and simulation algorithm. An annealing version of this algorithm was developed for real small protein folding problems. The numerical results indicate that it outperforms simulated annealing and conventional Monte Carlo algorithms as a stochastic optimization algorithm. We also propose one method for the use of secondary structures in protein folding. The predicted protein structures are rather close to the true structures. Phylogenetic trees have b

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Luczynska, Marta Magdalena. "Markov chain Monte Carlo and its applications to phylogenetic tree construction." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/62989.

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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 93-96).<br>This thesis addresses the application of Bayesian methods to problems in phylogenetics. Specifically, we focus on using genetic data to estimate phylogenetic trees representing the evolutionary history of genes and species. Knowledge of this common ancestry has implications for the identification of functions and properties of genes, the effect of mutations and their roles in particula

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He, Jintai. "MULTIPLE SEQUENCES ALIGNMENT FOR PHYLOGENETIC TREE CONSTRUCTION USING GRAPHICS PROCESSING UNITS." Available to subscribers only, 2008. http://proquest.umi.com/pqdweb?did=1674095441&sid=1&Fmt=2&clientId=1509&RQT=309&VName=PQD.

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Thesis (M.S.)--Southern Illinois University Carbondale, 2008.<br>"Department of Computer Science." Keywords: GPU computing, Sequence alignment. Includes bibliographical references (p. 34). Also available online.

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Jones, Todd R. "SigTree: An Automated Meta-Analytic Approach to Find Significant Branches in a Phylogenetic Tree." DigitalCommons@USU, 2012. https://digitalcommons.usu.edu/etd/1314.

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An experiment involving two treatment groups compared whole wheat diet and refined wheat diet on different sets of mice. Of interest were the differences by treatment of the levels of hundreds of bacteria in the guts of the mice. It was desired to determine the statistical significance of not only the individual bacteria, but also the families of bacteria. These family relationships are represented in a phylogenetic tree, and it was determined helpful to color the branches of bacteria based on the significance of their corresponding families. Calculating these p-values and coloring the branche

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Hime, Paul Michael. "GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES." UKnowledge, 2017. http://uknowledge.uky.edu/biology_etds/45.

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Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation e

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Tsang, John. "An Approximation Algorithm for Character Compatibility and Fast Quartet-based Phylogenetic Tree Comparison." Thesis, University of Waterloo, 2000. http://hdl.handle.net/10012/1110.

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Phylogenetic analysis, or the inference of evolutionary history is done routinely by biologists and is one of the most important problems in systematic biology. In this thesis, we study two computational problems in the area. First, we study the evolutionary tree reconstruction problem under the character compatibility (CC) paradigm and give a polynomial time approximation scheme (PTAS) for a variation of the formulation called fractional character compatibility (FCC), which has been proven to be NP-hard. We also present a very simple algorithm called the Ordinal S

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23

Dnyansagar, Rohit. "Investigation of phylogenetic relationships using microRNA sequences and secondary structures." Thesis, Högskolan i Skövde, Institutionen för vård och natur, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-4478.

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MicroRNAs are important biomolecules for regulating biological processes. Moreover, the secondary structure of microRNA is important for its activity and has been used previously as a mean for finding unknown microRNAs. A phylogenetic study of the microRNA secondary structure reveals more information than its primary sequence, because the primary sequence can undergo mutations that give rise to different phylogenetic relationships, whereas the secondary structure is more robust against mutations and therefore sometimes more informative. Here we constructed a phylogenetic tree entirely based o

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Stewart, Jane, Lavern Timmer, Christopher Lawrence, Barry Pryor, and Tobin Peever. "Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen." BioMed Central, 2014. http://hdl.handle.net/10150/610386.

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BACKGROUND:Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used<br>however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histo

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25

Harcourt-Brown, Katherine Grace. "Phylogenetic tree shape : with special reference to the phylogeny of the Cretaceous globotruncanid foraminifera." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.392962.

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26

Hill, Tobias. "Development of New Methods for Inferring and Evaluating Phylogenetic Trees." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7501.

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27

Chen, Xing. "EVOLUTION OF GROUP I INTRONS IN THE NUCLEAR RIBOSOMAL RNA GENES OF DOTHIDEOMYCETES." Bowling Green State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1288376350.

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28

Keller-Schmidt, Stephanie. "Stochastic Tree Models for Macroevolution." Doctoral thesis, Universitätsbibliothek Leipzig, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-96504.

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Phylogenetic trees capture the relationships between species and can be investigated by morphological and/or molecular data. When focusing on macroevolution, one considers the large-scale history of life with evolutionary changes affecting a single species of the entire clade leading to the enormous diversity of species obtained today. One major problem of biology is the explanation of this biodiversity. Therefore, one may ask which kind of macroevolutionary processes have given rise to observable tree shapes or patterns of species distribution which refers to the appearance of branching orde

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29

Rokas, Antonis. "Tree-thinking, molecules and gallwasps : analysing evolutionary patterns in European gallwasps using a molecular phylogenetic approach." Thesis, University of Edinburgh, 2001. http://hdl.handle.net/1842/14315.

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I have analysed data from nuclear and mitochondrial DNA sequence data in gallwasps and reviewed rare large-scale mutational changes in animals, in an attempt to understand their utility for phylogenetic analysis. Analysis of the sequence data led to the identification of fast and slow-evolving loci for insect phylogenetics. Review of published data on rare large-scale mutations (or Rare Genomic Changes - RGCs for short) suggested that RGCs are likely to be useful and low-homoplasy phylogenetic markers. Using DNA sequence and allozyme data, I studied the phylogeography and post-Pleistocene rang

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30

Inthara, Chantip. "Phylogenetic relationships among tree frogs of the genera Polypedates and Rhacophorus : an analysis of morphological data." Paris, Muséum national d'histoire naturelle, 2009. http://www.theses.fr/2009MNHN0015.

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Cladistic analyses of morphological data support a monophyletic group for Polypedates but do not support a monophyletic group for Rhacophorus. Five groups of Rhacophorus are recognized:(1) Group I: R. Appendiculatus; R. Verrucosus; R. Bisacculus; R. Everetti; R. Baliogaster and R. Cavirostris. DIAGNOSIS: post cloacal region with tubercles and/or papillae; skin on dorsum with glandular warts; tip of fingers and toes round; webbing between fingers III-IV small; dermal ridge running along outer edge of fourth finger crenulated; presence of numerous small papillae on heel; dermal ridge running alo

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Botte, Marco [Verfasser], Anita [Akademischer Betreuer] Schöbel, Anita [Gutachter] Schöbel, and Stephan [Gutachter] Huckemann. "Facility Location in the Phylogenetic Tree Space / Marco Botte ; Gutachter: Anita Schöbel, Stephan Huckemann ; Betreuer: Anita Schöbel." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://d-nb.info/1182033555/34.

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Fang, Qixun. "Predicting functional alterations caused by non-synonymous variants in CHO using models based on phylogenetic tree and evolutionary preservation." Thesis, University of Sheffield, 2018. http://etheses.whiterose.ac.uk/21624/.

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Chinese Hamster Ovary (CHO) cell is a major manufacturing platform for one of the most valuable biopharmaceutical products: monoclonal antibodies. Being an immortal cell line adapted to different environments, CHO has been accumulating massive mutations in its genome. Continuous effort has been invested into building a computational model to predict CHO cell productivity. However, not much attention has been focused on its proteins which are surely effected by the mutations accumulated to some extent. In this project, we focused on the functional effect caused by non-synonymous variants found

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33

Deng, Ziling. "Phylogenetic analysis of aquatic microbiomes : Evolution of the brackish microbiome." Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278730.

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Microorganisms play crucial roles in aquatic environments in determining ecosystemstability and driving the turnover of elements essential to life. Understanding thedistribution and evolution of aquatic microorganisms will help us predict how aquaticecosystems will respond to Global Change, and such understanding can be gained bystudying these processes of the past. In this project, we investigate the evolutionaryrelationship between brackish water bacteria from the Baltic Sea and Caspian Seawith freshwater and marine bacteria, with the goal of understanding how brackishwater bacteria have evo

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Miller, Justin B. "Analyzing Codon Usage and Coding Sequence Length Biases Across the Tree of Life." BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7603.

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Although codon usage bias has been shown to persist through non-random mutations and selection, many avenues of research into the applications of codon usage bias have remained unexplored. In this dissertation, we present several new applications of codon usage bias and their practical uses in a phylogenetic construct. We first review the literature and provide background into other software applications of codon usage bias in Chapter 1. In Chapter 2, we show that in tetrapods, codon aversion in orthologs is phylogenetically conserved. We further this analysis in Chapter 3 by exploring codon u

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Hartmann, Klaas. "Biodiversity conservation and evolutionary models." Thesis, University of Canterbury. Mathematics and Statistics, 2008. http://hdl.handle.net/10092/1776.

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Biodiversity conservation requires a framework for prioritising limited resources to the many endangered species. One such framework that has seen much attention and is considered extensively in this thesis, is the Noah's Ark Problem (NAP). The NAP combines a biodiversity measure (Phylogenetic Diversity; PD) with species survival probabilities and conservation costs. The aim of the NAP is to allocate the limited conservation resources such that the future expected PD is maximised. Obtaining optimal solutions to the NAP is a computationally complex problem to which several efficient algorithms

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Chang, Jia-Ming 1978. "Influence of alignment uncertainty on homology and phylogenetic modeling." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/129301.

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Most evolutionary analyses are based upon pre-estimated multiple sequence alignment models. From a computational point of view, it is too complex to estimate a correct alignment, as it is to derive a correct tree from that alignment. Several works have recently reported on the influence of alignment on downstream analysis, and on the uncertainty inherent to their estimation. Chapter 1 develops the notion of alignment uncertainty as either inherent to the data (internal) or resulting from methodological biases (external). Chapter 2 presents two contributions of mine for the improvement o

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Ates, Mevlude Alev. "Molecular Phylogenetics Of Turkish Abies (pinaceae)species Based On Matk Gene Regions Of Chloroplast Genome." Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613642/index.pdf.

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Pineacea is the largest family of conifers that includes 51 species of Abies which is the second largest genus after Pinus. There are six native taxa in Turkey belonging to this genus. Four of these taxa (Abies cilicica subsp. isaurica, Abies nordmanniana subsp. bornm&uuml<br>lleriana, Abies nordmanniana subsp. equi-trojani, Abies x olcayana) are endemic and considered as low risk (LR) species according to the IUCN criteria. To determine the phylogenetic relationship in Abies spp. in Turkey, 18 populations of different taxa were collected from their natural distribution areas in Turkey. The ma

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Virel, Ana. "Molecular characterization and evolution of alpha-actinin : from protozoa to vertebrates." Doctoral thesis, Umeå University, Chemistry, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-931.

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<p>alpha-actinin is a ubiquitous protein found in most eukaryotic organisms. The ability to form dimers allows alpha-actinin to cross-link actin in different structures. In muscle cells alpha-actinin is found at the Z-disk of sarcomeres. In non-muscle cells alpha-actinin is found in zonula adherens or focal adhesion sites where it can bind actin to the plasma membrane.</p><p>alpha-actinin is the shortest member of the spectrin superfamily of proteins which also includes spectrin, dystrophin and utrophin. Several hypotheses suggest that alpha-actinin is the ancestor of this superfamily.</p><p>T

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Duarte, Tharlley Rodrigo Eugenio. "Diagnóstico e filogenia molecular dos vírus da febre amarela a partir de amostras humanas negativas para os vírus dengue." Universidade Federal de Goiás, 2018. http://repositorio.bc.ufg.br/tede/handle/tede/8475.

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Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2018-05-15T11:01:10Z No. of bitstreams: 2 Dissertação - Tharlley Rodrigo Eugenio Duarte - 2018.pdf: 3238895 bytes, checksum: 4372ea2b66d739dd3a82a02b57e2b24a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5)<br>Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-05-15T12:24:47Z (GMT) No. of bitstreams: 2 Dissertação - Tharlley Rodrigo Eugenio Duarte - 2018.pdf: 3238895 bytes, checksum: 4372ea2b66d739dd3a82a02b57e2b24a (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf842

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Tarawneh, Monther. "A Novel Quartet-Based Method for Inferring Evolutionary Trees from Molecular Data." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/2301.

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Molecular Evolution is the key to explain the divergence of species and the origin of life on earth. The main task in the study of molecular evolution is the reconstruction of evolutionary trees from sequences data of the current species. This thesis introduces a novel algorithm for inferring evolutionary trees from genetic data using quartet-based approach. The new method recursively merges sub-trees based on a global statistical provided by the global quartet weight matrix. The quarte weights can be computed using several methods. Since the quartet weights computation is the most expensive

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Tarawneh, Monther. "A Novel Quartet-Based Method for Inferring Evolutionary Trees from Molecular Data." University of Sydney, 2008. http://hdl.handle.net/2123/2301.

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octor of Philosophy(PhD)<br>Molecular Evolution is the key to explain the divergence of species and the origin of life on earth. The main task in the study of molecular evolution is the reconstruction of evolutionary trees from sequences data of the current species. This thesis introduces a novel algorithm for inferring evolutionary trees from genetic data using quartet-based approach. The new method recursively merges sub-trees based on a global statistical provided by the global quartet weight matrix. The quarte weights can be computed using several methods. Since the quartet weights comput

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ABDUL, MAHDI NOOR. "Genetic variability Of the LCR, E6, E7 and L1 genes of the high risk HPV-31, HPV-58 and probable high risk HPV-66, HPV-53 and Phylogenetic analysis of the infected Italian women from urban area of Rome." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2009. http://hdl.handle.net/2108/214311.

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Sono stati descritti oltre 100 genotipi HPV, 18 dei quali classificati come ad alto rischio a causa della loro associazione con lo sviluppo del cancro alla cervice. La diversità genomica all’interno dello stesso genotipo di HPV-16 e 18 è stata sudiata in maniera estesa, mentre pochi dati sono stati prodotti per altri genotipi meno comuni ad alto rischio. Il presente studio investiga la variabilità nucleotidica e la filogenesi dei genotipi ad alto rischio HPV-31e HPV58 e i probabili genotipi ad alto rischio HPV53 e HPV66 in campioni raccolti in Italia, a Roma. A questo scopo, i geni L1, E6, E7

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Aleksandra, Konjević. "Fauna stenica (Heteroptera) različitih ekosistema imolekularne karakteristike važnijih vrsta." Phd thesis, Univerzitet u Novom Sadu, Poljoprivredni fakultet u Novom Sadu, 2015. https://www.cris.uns.ac.rs/record.jsf?recordId=94732&source=NDLTD&language=en.

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Istraživanja faune stenica na prostoru Vojvodine uposlednjih nekoliko decenija baziraju se pre svega napraćenju brojnosti i &scaron;tetnosti vrsta u p&scaron;enici, lucerki isoji. Malo je podataka o korisnim vrstama, kao idrugim vrstama koji imaju mali ili gotovo beznačajanuticaj na biljnu proizvodnju. Stoga je u ovom raduistražena fauna stenica različitih ekosistema kojiobuhvataju useve p&scaron;enice i lucerke, ali i biljkeruderalnih stani&scaron;ta i poljoza&scaron;titnih pojaseva navedenihkultura. Istovremeno je istražena i fauna stenica sabiljaka spontane flore na lokalitetima vi&scaron;i

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Martijn, Joran. "Exploration of microbial diversity and evolution through cultivation independent phylogenomics." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-327310.

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Our understanding of microbial evolution is largely dependent on available genomic data of diverse organisms. Yet, genome-sequencing efforts have mostly ignored the diverse uncultivable majority in favor of cultivable and sociologically relevant organisms. In this thesis, I have applied and developed cultivation independent methods to explore microbial diversity and obtain genomic data in an unbiased manner. The obtained genomes were then used to study the evolution of mitochondria, Rickettsiales and Haloarchaea. Metagenomic binning of oceanic samples recovered draft genomes for thirteen novel

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Vogel, Ivan. "Aplikace pro zpracování dat z oblasti evoluční biologie." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2011. http://www.nusl.cz/ntk/nusl-235533.

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Phylogenetic tree inference is a very common method for visualising evolutionary relationships among species. This work focuses on explanation of mathematical theory behind molecular phylogenetics as well as design of a modified algorithm for phylogenetic tree inference based on intra-group analysis of nucleotide and amino acid sequences. Furthermore, it describes the object design and implementation of the proposed methods in Python language, as well as its integration into powerful bioinformatic portal. The proposed modified algorithmic solutions give better results comparing to standard met

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Zembol, Filip. "Statistické vyhodnocení fylogeneze biologických sekvencí." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2013. http://www.nusl.cz/ntk/nusl-220015.

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The topic of my diploma thesis is the statistical evaluation of biological sequences with the help of phylogenic trees. In the theoretical part we will create a literary recherche of estimation methodology concerning the course of phylogeny on the basis of the similarity of biological sequences (DNA and proteins) and we will focus on the inaccuracies of the estimation, their causes and the possibilities of their elimination. Afterwards, we will compare the methods for the statistical evaluation of the correctness of the course of phylogeny. In the practical part of the thesis we will suggest a

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Oliveira, Olga Margarida Fajarda. "Network topology discovery." Doctoral thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/18692.

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Doutoramento em Matemática<br>A monitorização e avaliação do desempenho de uma rede são essenciais para detetar e resolver falhas no seu funcionamento. De modo a conseguir efetuar essa monitorização, e essencial conhecer a topologia da rede, que muitas vezes e desconhecida. Muitas das técnicas usadas para a descoberta da topologia requerem a cooperação de todos os dispositivos de rede, o que devido a questões e políticas de segurança e quase impossível de acontecer. Torna-se assim necessário utilizar técnicas que recolham, passivamente e sem a cooperação de dispositivos intermédios,

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Al-Nuaimi, Bashar. "Ancestral Reconstruction and Investigations of Genomics Recombination on Chloroplasts Genomes." Thesis, Bourgogne Franche-Comté, 2017. http://www.theses.fr/2017UBFCD042/document.

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La théorie de l’évolution repose sur la biologie moderne. Toutes les nouvelles espèces émergent d’une espèce existante. Il en résulte que différentes espèces partagent une ascendance commune, telle que représentée dans la classification phylogénétique. L’ascendance commune peut expliquer les similitudes entre tous les organismes vivants, tels que la chimie générale, la structure cellulaire, l’ADN comme matériau génétique et le code génétique. Les individus d’une espèce partagent les mêmes gènes mais (d’ordinaire) différentes séquences d’allèles de ces gènes. Un individu hérite des allèles de l

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Brantner, Emily K. "Regional evolutionary distinctiveness and endangerment as a means of prioritizing protection of endangered species." FIU Digital Commons, 2015. http://digitalcommons.fiu.edu/etd/2267.

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Conservation is costly, and choices must be made about where to best allocate limited resources. I propose a regional evolutionary diversity and endangerment (RED-E) approach to prioritization of endangered species. It builds off of the evolutionary diversity and global endangerment (EDGE) approach, but will allow conservation agencies to focus their efforts on species in specific regions. I used the RED-E approach to prioritize mammal and bird species listed under the U.S. Endangered Species Act (ESA), as well as to make a ranking of species without ESA critical habitat (CH), as a practical a

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Gibb, Gillian Claire. "Birds in a tree : a journey through avian phylogeny, with particular emphasis on the birds of New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics." Massey University, 2010. http://hdl.handle.net/10179/1329.

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Two main themes to the avian research presented in this thesis are, 1. Deep resolution of birds generally, and 2. Investigation of specific aspects of the New Zealand avifauna. More specifically, this thesis covers phylogeny, and predictions about palaeognaths, pigeons, pelecaniforms and passerines. Significant progress is made in resolving the basal branches of Neoaves. This thesis examines whether the six-way basal Neoavian split of Cracraft (2001) is, in principle, resolvable. New mitochondrial genomes are added to improve taxon sampling, break up long branches, and allow testing of the pri

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