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Implementacija metode asimetričnega srednjega drevesa za iskanje konsenza filogenetskih dreves : diplomsko delo
Soban, Urban (Author), Curk, Tomaž (Mentor) More about this mentor... This link opens in a new window

URLURL - Presentation file, Visit http://eprints.fri.uni-lj.si/2672/ This link opens in a new window

Abstract
Filogenetsko drevo prikazuje evolucijska razmerja med taksonomskimi enotami. Danes jih gradimo programsko z uporabo različnih metod in na podlagi različnih virov podatkov (npr., zaporedja DNA ali RNA). To mnogokrat privede do nasprotujočih si evolucijskih hipotez, ki jih nato skušamo združiti v eno samo hipotezo oziroma konsenzno drevo. V diplomskem delu je obravnavana konsenzna metoda asimetričnega srednjega drevesa. Le-ta in še dve aproksimacijski metodi so bile implementirane v odprtokodnem paketu Biopython. Uspešnost metode asimetričnega srednjega drevesa je bila primerjana z uspešnostjo metod za gradnjo striktnega, večinskega in Adamsovega konsenza, na nekaj umetnih in enem dejanskem primeru. Pridobljena drevesa so bila ovrednotena z uporabo Robinson-Fouldsove mere in mere razrešenosti drevesa. Asimetrično srednje drevo je velikokrat najmanj podobno vhodnim drevesom, a hkrati najbolj razrešeno drevo, saj podaja največ informacije o evolucijskih razmerjih med taksonomskimi enotami.

Language:Slovenian
Keywords:konsenz, drevo, filogenetika, asimetrično srednje drevo, Biopython, Robinson-Fouldsova mera, računalništvo, računalništvo in informatika, univerzitetni študij, diplomske naloge
Work type:Bachelor thesis/paper (mb11)
Tipology:2.11 - Undergraduate Thesis
Organization:FRI - Faculty of computer and information science
Year:2014
Publisher:[U. Soban]
Number of pages:63 str.
UDC:004.4:575(043.2)
COBISS.SI-ID:1536122051 This link opens in a new window
Views:598
Downloads:180
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Secondary language

Language:English
Title:Implementation of asymmetric median tree method for the computation of a consensus phylogenetic tree
Abstract:
A phylogenetic tree displays evolutionary relationships between taxonomical units. Nowadays, they are constructed programmatically by using different methods of inference and relying on various data sources, such as DNA and RNA sequences. The resulting evolutionary hypotheses are often contradictory, and need to be resolved by applying consensus methods. In this thesis, asymmetric median tree method (AMT) for construction of consensus phylogenetic trees is described, and along with two other approximation methods implemented in Biopython. AMT was compared to methods of strict, majority and Adams consensus trees on a number of artificial and one real data set. The comparisons were evaluated using the Robinson-Foulds and the tree resolution metrics. The results show that AMT is often the least similar to the input trees. At the same time, it is the most resolved tree, and therefore it offers the most information about evolutionary history of taxonomical units.

Keywords:consensus, tree, phylogeny, asymmetric median tree, Biopython, Robinson-Foulds distance, computer science, computer and information science, diploma

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