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* [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment | * [http://bio-bwa.sourceforge.net/ bwa] - Burrows-Wheeler Alignment Tool for efficient short read alignment - see [https://bugzilla.redhat.com/show_bug.cgi?id=597315] | ||
* [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> | * <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 | * [http://hannonlab.cshl.edu/fastx_toolkit/index.html FASTX-Toolkit] - Command line tools for Short-Reads FASTA/FASTQ files preprocessing - see [https://bugzilla.redhat.com/show_bug.cgi?id=597307] | ||
* [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.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats. | * [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats. | ||
Revision as of 16:06, 28 May 2010
- bwa - Burrows-Wheeler Alignment Tool for efficient short read alignment - see [1]
- 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 - see [2]
- GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
- 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
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.