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Dissertations / Theses on the topic 'Phylogenetic analysis'

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Published: 4 June 2021

Last updated: 25 July 2025

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1

Krig, Kåre. "Methods for phylogenetic analysis." Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.

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<p>In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix <em>d</em>.</p><p>In this thesis I present a few methods for constructing a phylogenetic tree from <em>d</em>. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a

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2

Gottschling, Marc. "Phylogenetic analysis of selected Boraginales." [S.l. : s.n.], 2003. http://www.diss.fu-berlin.de/2003/30/index.html.

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3

Boudko, Ekaterina. "Phylogenetic Analysis of Subtribe Alopecurinae (Poaceae)." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/30696.

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Subtribe Alopecurinae (Poeae, Poaceae) sensu lato‘s seven genera share interesting morphological similarities (dense spicate panicles and one-flowered spikelets) that were widely thought to have a common origin. However, recent molecular evidence for three of the genera has suggested that the subtribe may be polyphyletic. To test this, five DNA regions were sequenced and analyzed using phylogenetic methods. Results confirm that Alopecurinae s.l. as presently treated is polyphyletic and should be dissolved. Additionally, the genus Cornucopiae may be just another Alopecurus. Limnas and Pseudophl

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4

Williams, Annette Mary. "Phylogenetic analysis of the genus Streptococcus." Thesis, University of Reading, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333267.

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5

Högnabba, Filip. "Phylogenetic studies of cyanobacterial lichens /." Helsinki : Yliopistopaino, 2007. http://ethesis.helsinki.fi.

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6

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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7

Paquette, Lance. "Phylogenetic analysis of the bryozoan Suborder Rhabdomesina." Diss., Connect to online resource - MSU authorized users, 2008.

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8

Powell, Robyn Faye. "Systematics, diversification and ecology of the Conophytum-clade (Ruschieae; Aizoaceae)." University of the Western Cape, 2016. http://hdl.handle.net/11394/5453.

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Philosophiae Doctor - PhD<br>The Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum

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9

Park, Hyun Jung. "Large-scale analysis of phylogenetic search behavior." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1452.

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10

Msimanga, Wela Patrick. "Phylogenetic analysis of HIV-1 in Mpumalanga." Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80344.

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Thesis (MScMedSc)--Stellenbosch University, 2013.<br>The diversity of HIV-1 sequences derived from patients in Bushbuckridge, Mpumalanga, was investigated. The gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 51 patients were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was assigned using the LANL QC (RIP), REGA and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Most of the sequences, that is 89%, belonged to HIV-1 subtype C. LANL QC (RIP),

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11

Couto, Diogo Ribeiro do. "A PHYLOGENETIC ANALYSIS OF FASCIOLARIIDAE (GASTROPODA: BUCCINOIDEA)." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/38/38131/tde-08022017-214445/.

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The neogastropod family Fasciolariidae comprise of important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae, Fusininae and Peristerniinae. Fasciolariids with many well-known species such as tulip shells, horse-conchs, spindles, among others have a long complicated taxonomical history, with several genus names being used to group heterogeneous contingents of many unrelated species. Recently, however, taxonomical revisions have begun to set straight its taxonomy. The present work aims to resolve the phylogeny of the fa

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12

Robson, Brown Katharine Amanda. "A phylogenetic systematic analysis of homonid behaviour." Thesis, University of Cambridge, 1995. https://www.repository.cam.ac.uk/handle/1810/271944.

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13

AL-Saghir, Mohannad Ghazi. "Phylogenetic Analysis of the Genus Pistacia (Anacardiaceae)." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/28131.

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Pistacia is an economically important genus because it contains the pistachio crop, P. vera, which has edible seeds of considerable commercial importance. The evolutionary history of the genus and the taxonomic relationships among the species are controversial and not well understood. This study that has been conducted on this genus to refine taxonomic and evolutionary relationship utilizing different types of data (including morphology, anatomy and molecular) The studied species were the following: Pistacia aethiopica J. O. Kokwaro, P. atlantica Desf., P. chinensis Bunge, P. eurycarpa Yaltiri

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14

Lewis, Louise Ann. "Molecular phylogenetic analysis of Neochloris (Chlorophyceae, Chlorophyta) /." The Ohio State University, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487688507505424.

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15

Ferguson, Meg Elizabeth. "Statistical Analysis of Species Level Phylogenetic Trees." Bowling Green State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274.

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16

Jandhyam, Haritha Lakshmi. "Molecular phylogenetic analysis of novel spiroplasma isolates." Click here to access thesis, 2009. http://www.georgiasouthern.edu/etd/archive/spring2009/haritha_l_jandhyam/jandhyam_haritha_l_200901_ms.pdf.

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Thesis (M.S.)--Georgia Southern University, 2009.<br>"A thesis submitted to the Graduate Faculty of Georgia Southern University in partial fulfillment of the requirements for the degree Master of Science." Directed by Laura B. Regassa. ETD. Includes bibliographical references (p. 64-69) and appendices.

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17

Bauer, Jennifer E. "A Phylogenetic and Paleobiogeographic Analysis of the Ordovician Brachiopod Eochonetes." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1397486053.

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18

Habib, Farhat Abbas. "Genotype-phenotype correlation using phylogenetic trees." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187297400.

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19

MUNDELL, J. NICOLE. "PHYLOGENETIC ANALYSIS OF KENTUCKY STRAINS OF XYLELLA FASTIDIOSA." UKnowledge, 2005. http://uknowledge.uky.edu/gradschool_theses/406.

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Phytopathogenic bacterium, Xylella fastidiosa, causes a number of economically important diseases, including Pierces disease (PD) of grape and bacterial leaf scorch (BLS) of a number of landscape trees. In Kentucky (KY), BLS affects a number of shade trees including many oak and maple species. In 2001, PD was diagnosed in grapevines in western KY. Xylella fastidiosa is also detected in many asymptomatic landscape plants and grasses. It was the goal of this research to identify hosts of X. fastidiosa around KY and use phylogenetic analysis to compare sequences of the 16S rDNA and gyrase B (gyrB

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20

Martinez-Murcia, Antonio J. "Phylogenetic analysis of the genera Leuconostoc and Aeromonas." Thesis, University of Reading, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336137.

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21

Cai, Junpeng. "Molecular phylogenetic analysis on some ascomycetous spoilage yeasts." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297332.

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22

Sheehy, Robert Rowland. "A phylogenetic analysis of the Accipitridae (class Aves)." Diss., The University of Arizona, 1995. http://hdl.handle.net/10150/187367.

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The avian family Accipitridae is a large, diverse family composed of approximately 230 species divided into 56 genera. The evolutionary relationships among Acciptrid taxa have been examined previously using phenetic and parsimony approaches and a variety of data sets. These studies have resulted in conflicting phylogenies, presumably due to the high level of homoplasy, perhaps, the result of convergence on diet. To develop a firm understanding of the relationships among the major species groups (i.e., morphological types) an analysis of DNA sequence data from the mitochondrial encoded cytochro

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23

Antony, Lucille Marilyn May Kriger d'Amorim. "A phylogenetic analysis of the Rhodacaroidea (Acari: mesostigmata) /." The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487268021748041.

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24

Malosso, Elaine. "Effects of plant amendment on microbial community structure and fungal biomass in Antarctic soils." Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289240.

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25

Chamberlain, A. T. "A taxonomic review and phylogenetic analysis of Homo habilis." Thesis, University of Liverpool, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382041.

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26

Zhang, Jiajie [Verfasser]. "Models and algorithms for phylogenetic marker analysis / Jiajie Zhang." Lübeck : Zentrale Hochschulbibliothek Lübeck, 2015. http://d-nb.info/1074176758/34.

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27

Buendia, Patricia. "Phylogenetic analysis of within-host serially-sampled viral data." FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/2019.

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The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. Ne

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28

Graham, Sean W. "Phylogenetic analysis of breeding-system evolution in heterostylous monocotyledons." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0002/NQ27937.pdf.

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29

Wang, Jeremy R. "Analysis and Visualization of Local Phylogenetic Structure within Species." Thesis, The University of North Carolina at Chapel Hill, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3562960.

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<p> While it is interesting to examine the evolutionary history and phylogenetic relationship between species, for example, in a sort of "tree of life", there is also a great deal to be learned from examining population structure and relationships within species. A careful description of phylogenetic relationships within species provides insights into causes of phenotypic variation, including disease susceptibility. The better we are able to understand the patterns of genotypic variation within species, the better these populations may be used as models to identify causative variants and possi

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30

Broad, Gavin Roy. "Phylogenetic analysis of host utilisation patterns in parasitoid hymenoptera." Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368910.

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31

Savva, George Mario. "Towards a liklihood framework for whole genome phylogenetic analysis." Thesis, University of East Anglia, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426346.

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32

Pisani, Davide. "Comparing and combining trees and data in phylogenetic analysis." Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247894.

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33

Ho, Pangus. "Analysis of word-order universals using Bayesian phylogenetic inference." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/77015.

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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (p. 65-66).<br>This thesis examines the novel approach by Dunn et al. (2011) that employs the Bayesian phylogenetic inference to compute the Bayes Factors that determine whether the evolutions of a set of word-order traits in four language families are correlated or independent. In the first part of the thesis, the phylogenetic trees of the Indo-European and Bantu language families are reconstructed

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34

Cobbe, Neville Richard. "Phylogenetic and functional analysis of SMC4 in Drosophila melanogaster." Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/11994.

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35

Spencer, Marc Richard. "A Phylogenetic Analysis of the Basal Ornithischia (Reptilia, Dinosauria)." Bowling Green State University / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1185914798.

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36

Clark, Jonathan Bradley. "A molecular phylogenetic analysis of the intracellular bacteria rickettsiae /." The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487678444257197.

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37

Mowbray, Alison. "Molecular and phylogenetic analysis of a Bacillus thuringiensis genetic locus." Thesis, University of Cambridge, 1999. https://www.repository.cam.ac.uk/handle/1810/256731.

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The diptericidal $\textit{Bacillus thuringiensis}$ (Bt) ssp. $\textit{fukuokaensis}$ strains 84-I and 17A were investigated for the presence of novel Cry proteins. N-terminal amino acid, immunological and PCR analysis indicated that both strains contain a novel set of $\delta$-endotoxins. N-terminal amino acid sequence analysis indicated that the larger proteins from each strain (90 and 72-kDa of 84-I and 70 and 65-kDa of 17A) were related to the Cry proteins of Bt ssp. $\textit{israelensis}$(Bti). Immunoblotting experiments confirmed that Cry10A-type proteins were present in both strains alth

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38

Garnham, Janine B. "Parallelization of the maximum likelihood approach to phylogenetic inference /." Online version of thesis, 2007. http://hdl.handle.net/1850/4778.

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39

Lee, Michael Soon Yoong. "Evolutionary morphology of Pareiasaurs." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338262.

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40

Guarido, Milehna. "Identification and phylogenetic analysis of Aedes species (Diptera: Culicidae) and arboviruses associated with them across tropical and temperate regions of South Africa (2015-2018)." Thesis, University of Pretoria, 2020. http://hdl.handle.net/2263/78358.

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Emerging and re-emerging diseases have increased worldwide in incidence in the past decades. Of these emerging diseases 60.3% are caused by zoonotic pathogens of which 22.8% are arboviruses or arthropod borne viruses. Arboviruses are transmitted by hematophagous insects, especially moquitoes. Multiple factors such as human population growth, climate change and adaptations of certain Aedes mosquito vector species to urban environments and anthropophilic have been attributed to causing this rise in arboviral infections. In Southern Africa, zoonotic arboviruses belonging to the families Flaviviri

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41

Zhen, Zhao. "The Qphyl System: a web-based interactive system for phylogenetic analysis." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/2691.

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Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively inc

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42

Zhen, Zhao. "The Qphyl System: a web-based interactive system for phylogenetic analysis." University of Sydney, 2008. http://hdl.handle.net/2123/2691.

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Master of Science<br>Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very cruci

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43

Jong, Yde Sijbrand Diederick Maria de. "Systematic, phylogenetic and biogeographic studies of Atlantic seaweeds." [Leiden] The Netherlands : Rijksherbarium/Hortus Botanicus, Leiden University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/40701628.html.

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44

Garcia, Michael R. "Identification of novel nuclear markers for use in phylogenetic analysis." Tallahassee, Fla. : Florida State University, 2010. http://purl.fcla.edu/fsu/lib/digcoll/undergraduate/honors-theses/2181925.

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Thesis (Honors paper)--Florida State University, 2010.<br>Advisor: Dr. Gavin J.P. Naylor, Florida State University, College of Arts and Sciences, Dept. of Biology. Includes bibliographical references.

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45

Dunne, Emma Maria. "Investigations in trypanosome diversity and evolution using molecular phylogenetic analysis." Thesis, University of Bristol, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289775.

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46

Gooder, Stephen John. "A phylogenetic and vicariance analysis of some African forest mammals." Thesis, University of Liverpool, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359167.

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47

Costa, Helena Sofia Gomes. "Molecular and phylogenetic analysis of parapoxvirus in north American pinnipeds." Master's thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2019. http://hdl.handle.net/10400.5/18138.

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Dissertação de Mestrado Integrado em Medicina Veterinária<br>Parapoxvirus causes nodular lesions in the skin and mucosal membranes of diverse species of pinnipeds, worldwide. Seal parapoxvirus is currently categorized as a tentative species of the Parapoxvirus genus. Between 2009 and 2018, 22 samples were collected from 12 pinnipeds representing 5 different species (grey seal, harp seal, harbor seal, California sea lion and northern elephant seal) with clinical suspicion of parapoxvirus infection, from rehabilitation facilities on the east and west coast of the United States of America. The ai

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48

Curtis, Sarah Maureen. "Enhanced phylogenetic analysis and targeted search for the genus Kribbella." Doctoral thesis, University of Cape Town, 2015. http://hdl.handle.net/11427/15757.

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49

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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50

Dale, D. "Comparisons of parsimony and likelihood-based methods in phylogenetic analysis." Thesis, University College London (University of London), 2006. http://discovery.ucl.ac.uk/1445406/.

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This work provides a defence of the claim that likelihood based methods provide a better framework for performing phylogenetic analyses on molecular sequences than do parsimony based methods under the conditions studied. Novel work introduced in the thesis includes simulation studies that examine the performance oflikelihood based and parsimony based methods at high evolutionary distances. At these distances, many changes accumulate at a single site causing a catastrophic collapse in the performance of the parsimony analysis. In contrast a well understood mathematical theory involving the use

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