Software
This page lists software projects our group at the WWU is involved in. Most of them are hosted here, while others are hosted by cooperators. Note that this list also contains legacy software replaced by follow-up projects.
bioinfweb.commons.java
| Project home: | http://commons.bioinfweb.info/Java/ |
| Current version: | 3.4.0 (Nov 26, 2020 4:05:00 PM) |
| Developers / contributers: | Ben Stöver, Sarah Wiechers |
A Java library containing the shared components developed for different bioinfweb projects. These components are made publicly available under GNU LGPL 3.
JTreeSS
| Project home: | http://bioinfweb.info/JTreeSS/ |
| Current version: | (Jul 8, 2019 10:00:00 AM) |
| Developers / contributers: | Ben Stöver, Charlotte Schmitt |
A library that reads and interprets style sheets for phylogenetic trees in the TreeSS format and can apply them to any data model representing a phylogenetic tree.
JPhyloIO
| Project home: | http://bioinfweb.info/JPhyloIO/ |
| Current version: | 1.0.0 (Jun 12, 2019 3:30:00 PM) |
| Developers / contributers: | Ben Stöver, Sarah Wiechers, Kai Müller |
A Java library for event-based reading and writing of different phylogenetic file formats through a common interface.
TreeGraph 2
| Project home: | http://treegraph.bioinfweb.info/ |
| Current version: | 2.15.0 beta (Apr 26, 2019 8:35:00 PM) |
| Developers / contributers: | Ben Stöver, Sarah Wiechers, Kai Müller |
TreeGraph 2 is a graphical editor for phylogenetic trees that features a variety of formatting options for the elements of a tree. Moreover, it supports several (visible or invisible) annotations (e.g. support values) for every branch or node. These annotations can be imported from Nexus tree files or text files containing data in a table (e.g. exported from a spreadsheet program).
PhyDE 2
| Project home: | http://bioinfweb.info/PhyDE2/ |
| Current version: | 0.0.0 alpha (May 15, 2018 12:00:00 PM) |
| Developers / contributers: | Ben Stöver, Jonas Bohn, Sarah van Groen, Lara Kösters, Dietmar Quandt, Kai Müller |
A multiple sequence alignment editor for phylogenetic purposes based on the functionality of LibrAlign and JPhyloIO.
LibrAlign
| Project home: | http://bioinfweb.info/LibrAlign |
| Current version: | 0.9.0 (Apr 18, 2018 5:37:00 PM) |
| Developers / contributers: | Ben Stöver, Kai Müller |
LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data
AlignmentComparator
| Project home: | http://bioinfweb.info/AlignmentComparator |
| Current version: | 1.0.0 beta (Mar 1, 2018 12:20:00 PM) |
| Developers / contributers: | Ben Stöver, Kai Müller |
AlignmentComparator is a GUI application to efficiently visualize and annotate differences between alternative multiple sequence alignments of the same data set.
TIC
| Project home: | http://bioinfweb.info/TIC/ |
| Current version: | 3.0.2 (Feb 26, 2018 3:10:00 PM) |
| Developers / contributers: | Ben Stöver, Sarah Wiechers |
Toolkit independent components (TIC) - A Java library for creating GUI components for Swing and SWT
LeafNet
| Project home: | http://www.leafnet.pbarre.de/ |
| Current version: | 0.0.1 (Dec 22, 2016 4:00:00 PM) |
| Developers / contributers: | Pierre Barré, Ben Stöver, Kai Müller, Volker Steinhage |
Convolutional neural networks (CNN) used to identify plants from images of leaves.
GBOL5 web application
| Project home: | http://gbol5.de/ |
| Current version: | 0.0.1 (Mar 15, 2015 3:40:34 PM) |
| Developers / contributers: | Sarah Wiechers, Kai Müller |
Ruby on Rails application for mass assembly of primer reads generated in the GBOL5 project into contigs, auto-assignment of reads to isolates, specimens, species and management of specimens, target species, etc.
SeqState
| Project home: | http://bioinfweb.info/Software/SeqState |
| Current version: | 1.4.1 (Oct 2, 2008 11:00:00 PM) |
| Developer: | Kai Müller |
Primer design, sequence statistics, and indel coding according to various schemes
PhyDE
| Project home: | http://www.phyde.de/ |
| Current version: | 0.9951 (Mar 31, 2008 12:00:00 AM) |
| Developers / contributers: | Jörn Müller, Kai Müller, Dietmar Quandt |
System-independent editor for DNA and amino acid sequence alignments, designed to assist anybody interested in phylogenetic or other comparative analyses of sequence data
PRAP2
| Project home: | http://bioinfweb.info/Software/PRAP2 |
| Current version: | 2.0 (Dec 30, 2007 12:00:00 AM) |
| Developer: | Kai Müller |
Parsimony and likelihood ratchet analyses with PAUP*
GraphicMeasurer
| Project home: | http://gm.bioinfweb.info/ |
| Current version: | (Jan 2, 2007 1:53:11 PM) |
| Developers / contributers: | Ben Stöver, Horst Bleckmann |
GraphicMeasurer is a program that is able to analyze graphics and videos by locating and tracking objects (e.g. moving animals). The extracted geometric objects can be referenced with a spread-sheet-like result sheet language which allows to generate tables containing positions, angles or more complex data derived from the located objects.
TreeGraph
| Project home: | http://treegraph.bioinfweb.info/Version1 |
| Current version: | 1.0rc1 (Jul 19, 2006 12:00:00 AM) |
| Developers / contributers: | Jörn Müller, Kai Müller |
Automated drawing of phylogenetic trees using an extensible tree description format
IndelCoder
| Project home: | http://bioinfweb.info/Software/IndelCoder |
| Current version: | 0.5 (Aug 30, 2005 12:00:00 AM) |
| Developer: | Kai Müller |
Automates encoding of indels according to 10 different schemes, including simple binary and complex matrix character schemes.
Note that IndelCoder is not available for download anymore, since all its functionality has been moved to SeqState.
PRAP
| Project home: | http://bioinfweb.info/Software/PRAP |
| Current version: | 1.0 (Jul 12, 2005 12:00:00 AM) |
| Developer: | Kai Müller |
Precursor of PRAP2. Parsimony ratchet analyses with PAUP* including random addition cycles of the ratchet and calculation of Bremer support applying the ratchet.
PRAT
| Project home: | http://bioinfweb.info/Software/PRAT |
| Current version: | 0.99 (Apr 15, 2004 12:00:00 AM) |
| Developer: | Kai Müller |
The command-line precursor of PRAP. (Note: PRAP2 is recommended as much more user-friendly version.)
QuickAlign
| Project home: | http://bioinfweb.info/Software/QuickAlign |
| Current version: | 1.03 (Jan 2, 2004 12:00:00 AM) |
| Developers / contributers: | Jörn Müller, Kai Müller |
Alignment editor for Macinthosh computers
GRate
| Project home: | http://bioinfweb.info/Software/GRate |
| Current version: | 1.0 (May 6, 2003 12:00:00 AM) |
| Developer: | Kai Müller |
Relative Rate Test for Groups of Taxa Using General DNA Substitution Models in PAUP*
