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Master thesis: Development and implementation of software components increasing the accessibility of phylogenetic metadata


Status finished on 2016-09-30
Student Wiechers, Sarah
Supervisors Müller, Kai
Bartelheimer, Maik
Stöver, Ben
Accepting institution Evolution and Biodiversity of Plants
Institute for Evolution and Biodiversity
WWU Münster
Hüfferstraße 1
48149 Münster
Germany
URL http://www2.ieb.uni-muenster.de/EvolBiodivPlants/Theses/Software_Components_Phylogenetic_Metadata.pdf

Abstract

With the amount of data produced in the field of phylogenetics growing larger every day one of the big challenges is to maintain this data and make it available for future use. A variety of different file formats, either wide-spread or specific to a single tool or software are currently available to store phylogenetic data. However, to be able to re-use previous results it is imperative that meaningful annotations about the contents of the file, the analysis methods and other helpful information about the contained phylogenies or multiple sequence alignments are attached. Many wide-spread phylogenetic file formats do not support the kind of rich annotations needed to fulfill these annotation standards. Additionally, interoperability between different phylogenetic tools is hindered by the variety of formats available and the large effort it takes to support all of them. This thesis aims to foster accessibility of phylogenetic data and metadata by implementing the support for four XML-based file formats in the Java library JPhyloIO, in addition to the existing support for various text-based formats. JPhyloIO can be used to provide full support of all included formats when developing new or extending existing software by just implementing a single reader and writer class. This greatly reduces the effort necessary to support a larger variety of different formats. JPhyloIO is still memory efficient when dealing with large data sets and can be combined with any application business model. Additionally, two features for the popular tree editor TreeGraph 2 are introduced, that allow importing and visualizing the results of an ancestral state reconstruction analysis and comparing different tree topologies as well as their statistical support visually. These results will hopefully help foster interoperability between phylogenetic tools and the accessibility of metadata by facilitating the use of more powerful file formats.

Publications

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Conference abstract (poster)

Stöver BC, Wiechers S, Müller KF: JPhyloIO - A Java library for event-based reading and writing of different alignment and tree formats through one common interface. European Conference on Computational Biology (ECCB); The Hague, The Netherlands; 2016 (Details)

Wiechers S, Müller KF, Stöver BC: New comparison and annotation methods of the phylogenetic tree editor TreeGraph 2. 5th annual Münster Graduate School of Evolution Symposium; Münster, Germany; 2015 (Details)

Stöver BC, Wiechers S, Müller KF: Recent development of the phylogenetic tree editor TreeGraph 2. German Conference on Bioinformatics (GCB); Dortmund, Germany; 2015 (Details)

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