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Software


This page lists the software projects our group is involved in. Note that all our software is hosted at the BioInfWeb project, the central software site managed by Kai Müller and Ben Stöver. You can find detailed user and developer documentations to most of the projects there, if you follow the links below. Additionally formal definitions of the XML formats used in our software is privided on BioInfWeb.

LibrAlign

Project home:   http://bioinfweb.info/LibrAlign
Current version:   0.4.0 (2017-01-18 20:15:00.0)
Developers / contributers:   Ben Stöver, Kai Müller

LibrAlign - A GUI library for displaying and editing multiple sequence alignments and attached data


TIC

Project home:   http://bioinfweb.info/TIC/
Current version:   2.0.0 (2017-01-17 18:10:00.0)
Developers / contributers:   Ben Stöver, Sarah Wiechers

Toolkit independent components (TIC) - A Java library for creating GUI components for Swing and SWT


TreeGraph 2

Project home:   http://treegraph.bioinfweb.info/
Current version:   2.13.0 beta (2017-01-09 16:25:00.0)
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).


bioinfweb.commons.java

Project home:   http://commons.bioinfweb.info/Java/
Current version:   2.2.0 (2017-01-09 10:40:00.0)
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.


JPhyloIO

Project home:   http://bioinfweb.info/JPhyloIO/
Current version:   0.3.0 (2016-12-14 13:15:00.0)
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.


GBOL5 web application

Project home:   http://gbol5.de/
Current version:   0.0.1 (2015-03-15 15:40:34.0)
Developer:   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.


AlignmentComparator

Project home:   http://bioinfweb.info/AlignmentComparator
Current version:   0.0.0-alpha (2014-06-30 02:16:34.0)
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.


SeqState

Project home:   http://bioinfweb.info/Software/SeqState
Current version:   1.4.1 (2008-10-02 23:00:00.0)
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 (2008-03-31 00:00:00.0)
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 (2007-12-30 00:00:00.0)
Developer:   Kai Müller

Parsimony and likelihood ratchet analyses with PAUP*


GraphicMeasurer

Project home:   http://gm.bioinfweb.info/
Current version:   (2007-01-02 13:53:11.0)
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 (2006-07-19 00:00:00.0)
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 (2005-08-30 00:00:00.0)
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 (2005-07-12 00:00:00.0)
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 (2004-04-15 00:00:00.0)
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 (2004-01-02 00:00:00.0)
Developers / contributers:   Jörn Müller, Kai Müller

Alignment editor for Macinthosh computers


GRate

Project home:   http://bioinfweb.info/Software/GRate
Current version:   1.0 (2003-05-06 00:00:00.0)
Developer:   Kai Müller

Relative Rate Test for Groups of Taxa Using General DNA Substitution Models in PAUP*



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