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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
a tool to master DNA sequences, plasmids and restriction digests
The Wiley DNA Editor is a simple tool to handle DNA sequence information up to 100 kbp using java script in your browser window. The main idea is to install nothing but start cloning. Here we handle the development and the bug reports. The Wiley DNA Editor can be used from our homepage - or the files available in the download section.
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multiple alignments, short read alignments and graphs. Most major data formats are supported. Local and internet files can be loaded.
This project has moved to GitHub: https://github.com/GenomeView/genomeview
Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.
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User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files
Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.
dna2abc turns DNA sequences into musical sequences. The key feature is the rule editor; a rule is a regular expression paired with a Tcl script. dna2abc scans a DNA sequence, testing each regular expression: if it matches, the Tcl script is run.
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COB editor is a collaborative editor for biological ontology (e.g., Gene Ontology) building. Building on the idea of modular ontology from KR research, it supports multiple people to work on the same ontology.
DNAGalaxy is an attempt to produce an open-source bioinformatics software alternative to the expensive DNAStar Lasergene software. Its features currently include Blast and Entrez searching, a frontend to clustal and a sequence editor. It requires java1.5
Mars Eva Computing Environment is a JMF, JINI project that is used to provide a collaborative mission planning & execution environment for furture teams on Mars. This effort is part of a simulation for the Mars Society of Australia.
** IMPORTANT NOTICE ** 10 Feb 2006 Code is being moved to the SMI subversion repository (http://smi-protege.stanford.edu/svn/owl/trunk/) Project will continue to be open source. ProtegeOWL info at: http://protege.stanford.edu/overview/protege-owl.html