Software Components for increased Data Reuse and Reproducibility in Phylogenetics and Phylogenomics

Basic data of the doctoral examination procedure

Doctoral examination procedure finished at: Doctoral examination procedure at University of Münster

Period of time: 01/03/2011 - 13/12/2018

Status: completed

Candidate: Stöver, Ben

Doctoral subject: Biologie

Doctoral degree: Dr. rer. nat.

Awarded by: Department 13 - Biology

Supervisors: Müller, Kai; Quandt, Dietmar; Makalowski, Wojciech

Description

The software components developed in this thesis contribute to an increased reusability of scientific data and to a greater reproducibility of underlying studies by allowing unambiguous annotation with metadata (e.g., links to raw data or information on applied methods) and clear comparison of results from alternative methods for multiple sequence alignment and phylogenetic inference. The bioinformatical libraries JPhyloIO and LibrAlign provide fundamental and easily reusable functionality for developers, while the applications based on them offer solutions for end users. The Taxonomic Editor of the EDIT platform covers taxonomic data, while PhyDE 2 and AlignmentComparator offer respective functionality for multiple sequence alignments and related metadata. TreeGraph 2 provides required functionality for phylogenetic trees and is currently in wide use worldwide. All developed software is freely available at http://bioinfweb.info/Software. Full text: https://nbn-resolving.org/urn:nbn:de:hbz:6-96159516963

Promovend*in an der Universität Münster

Stöver, Ben

Group Evolution and Biodiversity of Plants (Prof. Müller)

Supervision at the University of Münster

Makalowski, Wojciech	Institute of Bioinformatics
Müller, Kai	Group Evolution and Biodiversity of Plants (Prof. Müller)

Projects in which the doctoral examination procedure takes/took place

Aufbau eines Sammlungs-Erschließungssystems für die nordhemisphärische Blütenpflanzengattung Campanula

Duration: 01/11/2013 - 31/10/2014

Funded by: DFG - Scientific Library Services and Information Systems

Type of project: Individual project

Publications resulting from doctoral examination procedure

JPhyloIO: A Java library for event-based reading and writing of different phylogenetic file formats through a common interface Stöver BC, Wiechers S, Müller KF (2019) In: BMC Bioinformatics, 20(1) Type of Publication: Research article (journal)
Software components for increased data reuse and reproducibility in phylogenetics and phylogenomics Stöver, BC (2018) Münster: (no publisher available). Type of Publication: Thesis (doctoral or post-doctoral)
The CDM Applied: Unit-Derivation, from Field Observations to DNA Sequences Plitzner P, Müller A, Güntsch A, Berendsohn WG, Kohlbecker A, Kilian N, Henning T, Stöver BC (2017) In: TDWG 2017 Annual Conference, Ottawa, Canada, . Type of Publication: Abstract in digital collection (conference)
Increasing data accessibility and reuse in phylogenetics by employing externally defined ontologies Wiechers S, Müller KF, Stöver BC (2017) In: 6th annual Symposium of the Münster Graduate School of Evolution, Münster, Germany. Type of Publication: Poster
JPhyloIO - A Java library for event-based reading and writing of different alignment and tree formats through one common interface Stöver BC, Wiechers S, Müller KF (2016) In: European Conference on Computational Biology (ECCB), Den Haag, Netherlands (Kingdom of the). Type of Publication: Poster