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(Add IGV: http://www.broadinstitute.org/igv/) |
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* [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 | ||
* [http://www.broadinstitute.org/igv/ Integrated 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. | * [http://www.chevreux.org/projects_mira.html MIRA] - Genome fragment assembler for sequencing projects classified as 'hard' due to high number of similar repeats. | ||
* [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. | * [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. | ||
Revision as of 00:26, 3 June 2010
- 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
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 (Review Request)
- GENtle - DNA restriction analysis and cloning tool similar to VectorNTI
- Integrated 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
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.