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Software
This page lists all biological software that has been developed by Ben Stöver and Kai Müller. Note that this list also contains programs which have been replaced by extended projects we started later on.
TreeGraph 2
| Project home: | http://treegraph.bioinfweb.info/ |
| Current version: | 2.0.x beta (Jul 29, 2010 1:55:00 PM) |
| Developers / contributers: | Ben Stöver, Kai Müller |
TreeGraph 2 is a graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your 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).
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*
TreeGraph
| Project home: | http://www.math.uni-bonn.de/people/jmueller/extra/treegraph/ |
| 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
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*
