Implementation of asymmetric median tree method for the computation of a consensus phylogenetic tree

Urban Soban (2014) Implementation of asymmetric median tree method for the computation of a consensus phylogenetic tree. EngD thesis.

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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.

Item Type:

Thesis (EngD thesis)

Keywords:

consensus, tree, phylogeny, asymmetric median tree, Biopython, Robinson–Foulds distance

Number of Pages:

Language of Content:

Slovenian

Mentor / Comentors:

Name and Surname	ID	Function
doc. dr. Tomaž Curk	299	Mentor

Link to COBISS:

http://www.cobiss.si/scripts/cobiss?command=search&base=51012&select=(ID=1536122051)

Institution:

University of Ljubljana

Department:

Faculty of Computer and Information Science

Item ID:

2672

Date Deposited:

12 Sep 2014 17:11

Last Modified:

18 Dec 2014 10:42

URI:

http://eprints.fri.uni-lj.si/id/eprint/2672

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