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(Add COPASI)
(fastx_toolkit now packaged)
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* [http://copasi.org/ COPASI] - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models
* [http://copasi.org/ COPASI] - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
* [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing ([https://bugzilla.redhat.com/show_bug.cgi?id=597307 Review Request])
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
* [https://sourceforge.net/projects/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
* [http://www.broadinstitute.org/igv/ Integrative Genomics Viewer] - java-based graphical genomics viewer (licensed under GPLv2)
* [http://www.broadinstitute.org/igv/ Integrative Genomics Viewer] - java-based graphical genomics viewer (licensed under GPLv2)

Revision as of 18:34, 30 November 2011

  • Autodock - Suite of automated molecular docking tools
  • Autodock Vina - Tool for drug discovery, molecular docking and virtual screening
  • COPASI - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models
  • Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
  • GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
  • Integrative Genomics Viewer - java-based graphical genomics viewer (licensed under GPLv2)
  • MIRA - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats.
  • NCBI BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
  • NCBI C Toolkit - NCBI libraries and tools for biology applications srpm here
  • NCBI C++ Toolkit - a new generation of NCBI libraries and tools for biology
  • pyQPCR - qPCR analysis tool
  • Staden - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
  • Taverna - Tool for automation of experimental workflows.