Lab

Kai F Müller's Lab

Featured projects (7)

Project
GBOL is a national network of various natural history museums and other biodiversity research institutions in Germany. The GBOL partners provide their professional taxonomic expertise and existing infrastructure (collections / biobanks, databases, bioinformatics platforms and laboratories) to comprehensively collect, catalog, describe, and sequence the animal, plant and fungi species in Germany. While the focus in GBOL during the first phase (2012-2015) was laid on the creation of a reference database, we will now also develop different applications of DNA barcoding in the second project phase (2016-2018). Sequence and metadata generated in GBOL will be integrated in the global barcode reference database " BOLD ". www.bolgermany.de
Project
AlignmentComparator is able to visually compare and annotate differences between alternative multiple sequence alignments (MSAs) of the same data set. This allows the researcher to decide which alternative alignments to take into account as the bases of e.g. a phylogenetic study or numerous other tasks. Manual alignment corrections can be visualized or a bioinformatician can determine the effect of changes made to a MSA algorithm. http://bioinfweb.info/AlignmentComparator/ https://github.com/bioinfweb/AlignmentComparator http://twitter.com/bioinfweb Legal notice: http://bioinfweb.info/AlignmentComparator/About Privacy Policy: http://bioinfweb.info/Privacy
Project
LibrAlign is a Java library providing flexible and powerful GUI components for displaying and editing multiple sequence alignments (MSAs) and attached raw and metadata. It supports creating both Swing and SWT GUIs (using http://bioinfweb.info/TIC/) and the alignment formats FASTA, Phylip, Nexus, NeXML, MEGA and PDE. All components are easily extendable by application or third-party developers. The documentation and JavaDocs are available here: http://bioinfweb.info/LibrAlign/Documentation. If you have further questions, don't hesitate to ask one in this project. http://bioinfweb.info/LibrAlign/ https://github.com/bioinfweb/LibrAlign http://twitter.com/bioinfweb Legal notice: http://bioinfweb.info/LibrAlign/About Privacy Policy: http://bioinfweb.info/Privacy
Project
JPhyloIO is Java library for reading and writing phylogenetic (alignment and tree) file formats. It's aim is to allow developers of bioinformatical applications access to various formats using a single interface, while being independent of the concrete application data model. The library supports event based I/O of NeXML, Nexus, PhyloXML, FASTA, Newick, Phylip, Extended Phylip, MEGA, PDE and XTG, including all metadata modeled by these formats. This project keeps you up to date on the development of JPhyloIO, new releases and publications. The documentation, including full JavaDocs and multiple example applications showing how to use JPhyloIO are available here: http://bioinfweb.info/JPhyloIO/Documentation. If you have further questions, don't hesitate to ask one in this project. The project is open source under GNU LGPL. Suggestions and contributions (e.g. via GitHub) are always welcome. http://bioinfweb.info/JPhyloIO/ https://twitter.com/bioinfweb https://github.com/bioinfweb/JPhyloIO Legal notice: http://bioinfweb.info/JPhyloIO/About Privacy Policy: http://bioinfweb.info/Privacy
Project
This project keeps you up to date on the further development of TreeGraph 2, new releases and features. TreeGraph 2 is an easy to use editor for phylogenetic trees that offers a variety of editing and formatting options. You can interactively compare and combine trees from different (conflicting) analyses and attach an unlimited number of numerical or textual annotations to every node and branch. Newick, Nexus, NeXML, PhyloXML, tables and MrBayes data are supported for I/O. A complete documentation and tutorials are available here: http://treegraph.bioinfweb.info/Help. If you have further questions, don't hesitate to ask one in this project. http://treegraph.bioinfweb.info/ https://github.com/bioinfweb/TreeGraph2 http://twitter.com/bioinfweb Legal notice: http://treegraph.bioinfweb.info/About Privacy Policy: http://bioinfweb.info/Privacy

Featured research (1)

Background: Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata representation. Although most currently available software only supports the classical formats with a limited metadata model, it would be desirable to have support for the more advanced formats. This is necessary for users to produce richly annotated data that can be efficiently reused and make underlying workflows easily reproducible. A programming library that abstracts over the data and metadata models of the different formats and allows supporting all of them in one step would significantly simplify the development of new and the extension of existing software to address the need for better metadata annotation. Results: We developed the Java library JPhyloIO, which allows event-based reading and writing of the most common alignment and tree/network formats. It allows full access to all features of the nine currently supported formats. By implementing a single JPhyloIO-based reader and writer, application developers can support all of these formats. Due to the event-based architecture, JPhyloIO can be combined with any application data structure, and is memory efficient for large datasets. JPhyloIO is distributed under LGPL. Detailed documentation and example applications (available on http://bioinfweb.info/JPhyloIO/) significantly lower the entry barrier for bioinformaticians who wish to benefit from JPhyloIO's features in their own software. Conclusion: JPhyloIO enables simplified development of new and extension of existing applications that support various standard formats simultaneously. This has the potential to improve interoperability between phylogenetic software tools and at the same time motivate usage of more recent metadata-rich formats such as NeXML or phyloXML.

Lab head

Kai F Müller
Department
  • Institute for Evolution and Biodiversity

Members (2)

Ben C Stöver
  • University of Münster
Sarah Wiechers
  • University of Münster

Alumni (1)

Jonas Bohn
  • University of Münster