Bioinformatics Support and Documentation :: Command line tools
The Center for Genomics and Bioinformatics provides access to several bioinformatics analysis software through the
command line. A CGB Research Computing account is required to access the software.
To request an account please use our support form.
Command-line tools Overview
The following is a collection of all bioinformatics software installed and
supported by The Center for Genomics and Bioinformatics. Anyone having CGB Research Computing account can use the
software by following appropriate instructions. If you wish to use a tool not
present in this list, please send us a request.
Command-line tools Usage
A user can simply type 'use software_name' to initialize the environment and
then directly use the appropriate command. For instance if you wish to run some
emboss commands, you will type 'use emboss' on the terminal prompt, and then
use the appropriate tool from emboss suite by running its command, like 'transeq'.
A user can also type 'use -l' to see all the available software.
Another way is to directly include a group of software. A group of software is
initialized the same way as a single software by executing 'use group_name', eg.
'use alignment'.
| alignment |
Alignment tools
|
| est |
EST analysis tools
|
| gene-finding |
Gene search tools
|
| oligo |
Oligo design tools
|
| other |
Misc tools
|
| phred-phrap |
Phred-Phrap Sequencing tools
|
| phylogeny |
Phylogeny tools
|
| sequence |
Sequence format and Analysis
|
| molbio |
All the tools
Initialize the entire set of bioinformatics tools on research by just
typing 'use molbio'
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