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  Efficient estimation of evolutionary distances

Klötzl, F. (2015). Efficient estimation of evolutionary distances. Master Thesis, Universität zu Lübeck, Institut für Neuro- und Bioinformatik, Lübeck.

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https://github.com/EvolBioInf/andi (Supplementary material)
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The andi program for estimating the evolutionary distance between closely related genomes.
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 Creators:
Klötzl, Fabian1, Author           
Haubold, Bernhard1, Referee           
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1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445644              

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 Abstract: The advent of high throughput sequencers has lead to a dramatic increase in the size of
available genomic data. Standard methods, which have worked well for many years, are
not suitable for the analysis of big data sets, due to their reliance on a time-consuming
alignment step. In this thesis, a new alignment-free approach for phylogeny reconstruction is
introduced. The corresponding program, andi, is orders of magnitude faster than classical
approaches and also superior to comparable alignment-free methods.
The central data structure in andi is the enhanced suffix array. It is used to find long
exact matches between sequences. In this thesis, various approaches to the construction of
enhanced suffix arrays, including novel ones, are evaluated with respect to performance.
Additionally, a new parallel algorithm for the computation of suffix arrays is introduced.

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Language(s): eng - English
 Dates: 2015-04-012015-04-01
 Publication Status: Issued
 Pages: 63
 Publishing info: Lübeck : Universität zu Lübeck, Institut für Neuro- und Bioinformatik
 Table of Contents: -
 Rev. Type: -
 Identifiers: Other: Dipl/12632
 Degree: Master

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