SIGs/SciTech/BioinformaticsWishList

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(Move here Autodock and Autodock Vina. Delete 2 old entries)
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* [http://autodock.scripps.edu/ Autodock] Suite of automated molecular docking tools
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* [http://vina.scripps.edu/ Autodock Vina] Tool for drug discovery, molecular docking and virtual screening
 
* [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment ([https://bugzilla.redhat.com/show_bug.cgi?id=597315 Review Request])
 
* [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment ([https://bugzilla.redhat.com/show_bug.cgi?id=597315 Review Request])
 
* [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
* <strike>[http://emboss.sourceforge.net/ EMBOSS] - Hundreds of useful, well documented applications for molecular sequence and other analyses.</strike>
 
 
* [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])
 
* [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
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* [http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/ NCBI C++ Toolkit ] - a new generation of NCBI libraries and tools for biology  
 
* [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
 
* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool
* <strike>[http://samtools.sourceforge.net/ SAMtools] - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.</strike>
 
 
* [http://staden.sourceforge.net/ Staden]  - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
 
* [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.mygrid.org.uk/tools/taverna/ Taverna] - Tool for automation of experimental workflows.

Revision as of 15:34, 24 November 2010

  • Autodock Suite of automated molecular docking tools
  • Autodock Vina Tool for drug discovery, molecular docking and virtual screening
  • bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment (Review Request)
  • Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
  • FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing (Review Request)
  • 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.