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* [http://maq.sourceforge.net/bwa-man.shtml bwa] - Burrows-Wheeler Alignment Tool  
* [http://vina.scripps.edu/ Autodock Vina] - Tool for drug discovery, molecular docking and virtual screening. There's a package under http://copr.fedoraproject.org/coprs/loveshack/livhpc/
* [http://emboss.sourceforge.net/ EMBOSS package] - Hundreds of useful, well documented applications for molecular sequence and other analyses.
* <del>[http://copasi.org/ COPASI] - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models</del> See [https://admin.fedoraproject.org/pkgdb/package/rpms/COPASI/ COPASI]
* [http://staden.sourceforge.net/ Staden package] - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
* [http://www.cytoscape.org/ Cytoscape] - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI-BLAST and other tools] - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
* [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.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats. Uses '''non-free jlfgr''' -- see Debian packaging.
* [ftp://ftp.ncbi.nih.gov/toolbox/ NCBI BLAST and other tools] - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
** ncbi-blast+ packaged by jkaluza - https://bugzilla.redhat.com/show_bug.cgi?id=999383
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/INDEX.HTML NCBI C Toolkit ] - NCBI libraries and tools for biology applications [http://www.environnement.ens.fr/perso/dumas/fc-srpms/ncbi-6.1.20081116a-1.fc10.src.rpm srpm here]
* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ NCBI C++ Toolkit ] - a new generation of NCBI libraries and tools for biology
* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool
* [http://staden.sourceforge.net/ Staden] - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
* [http://www.mygrid.org.uk/tools/taverna/ Taverna] - Tool for automation of experimental workflows.
* [http://www.physionet.org/physiotools/wfdb.shtml The WFDB Software Package] - Software for viewing, analyzing, and creating recordings of physiologic signals


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Latest revision as of 11:18, 26 December 2015

  • Autodock Vina - Tool for drug discovery, molecular docking and virtual screening. There's a package under http://copr.fedoraproject.org/coprs/loveshack/livhpc/
  • COPASI - Simulation and analysis of biochemical networks and their dynamics, supports SBML standard for models See COPASI
  • 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. Uses non-free jlfgr -- see Debian packaging.
  • 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.
  • The WFDB Software Package - Software for viewing, analyzing, and creating recordings of physiologic signals
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