Software components for increased data reuse and reproducibility in phylogenetics and phylogenomics

Stöver, BC

Abstract

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.