- PhyDE 2 (http://bioinfweb.info/PhyDE2/)
Recently the libraries LibrAlign and JPhyloIO have been developed in our group. They provide powerful components for displaying, editing, reading and writing multiple sequence alignments and are already used in a number of applications.
In contrast to other available alignment editors, PhyDE, which is also developed in our group, focuses on multiple sequence alignment for phylogenetic purposes and offers respective specialized functionality. The goal of this thesis is to develop a new version of PhyDE that makes use of the new functionality already implemented in LibrAlign and JPhyloIO and adopts the features available in the Taxonomic EDITor, which is also based on LibrAlign and JPhyloIO.
Depending on the type and the progress of the thesis a follow-up task can be to add functionality for displaying and editing of raw- and metadata attached to alignments and sequences. LibrAlign allows to attach special GUI elements to each sequence (data areas), which can be implemented as plug-ins. This would allow PhyDE to display types of data that are not modeled by it directly. Such externally defined data areas would be the counterpart of metadata attached to sequences using externally defined RDF predicates as they are used e.g. in the NeXML format. Examples for such raw- and metadata are sequencing raw data (e.g. trace files or probability values for each nucleotide), information on secondary structure or repeat patterns, gene annotations an many more. (See also here for more detailed information on attaching metadata using RDF.)
Screenshot of the current version of PhyDE.
What we offer
- Individualized supervision and an advanced training in scientific software development.
- The opportunity to contribute to software that is well-established in the scientific community, so that a large number of users will directly benefit from your work.
- Co-authorship in a journal publication.
- Interest in working in bioinformatics.
- Knowledge of a programming language. (Object orientation/Java would be perfect, but not obligatory.)
- PhyDE website
- Conference poster describing LibrAlign
- Conference poster describing JPhyloIO
- Software developed in our group
If you are interested to work on this topic in your bachelor or master thesis or in a master research module, please contact Ben Stöver. (Working on other bioinformatics topics related to research and software is also possible.)