SIGs/SciTech/BioinformaticsWishList: Difference between revisions

Revision as of 11:06, 26 May 2010

bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment
Cytoscape - Platform for the analysis and visualization of complex networks, in particular molecular interaction networks and biological pathways
~~EMBOSS - Hundreds of useful, well documented applications for molecular sequence and other analyses.~~
FASTX-Toolkit - Command line tools for Short-Reads FASTA/FASTQ files preprocessing
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.
~~SAMtools - SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Tools for sorting, merging etc. sam format files.~~
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.
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
GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
pyQPCR - qPCR analysis tool

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 * [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/gentle-m/ GENtle] - DNA restriction analysis and cloning tool similar to VectorNTI
+* [https://sourceforge.net/projects/pyqpcr/ pyQPCR] - qPCR analysis tool
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