EMBOSS

Category(ies): Bioinformatics

Version: 4.0 (updated at 11/21/2006)
Old version emboss 3.0 is still available and moved to at
/usr/local/emboss-3.0

Author / Distributor:

Rice, P. Longden, I. and Bleasby, A.

Description:

Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:

Sequence alignment,
Rapid database searching with sequence patterns,
Protein motif identification, including domain analysis,
Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
Codon usage analysis for small genomes,
Rapid identification of sequence patterns in large scale sequence sets,
Presentation tools for publication,

and much more.

Emboss is dynamically maintaining a list of programs. Details are available at http://emboss.sourceforge.net/apps/
and http://emboss.sourceforge.net/apps/cvs/groups.html.

altix: running program | Documentation | Installation | System

Running Program:

Running the various applications by type the application name, i.e.

emma

to start multiple alignment program.

The EMBOSS command syntax follows normal UNIX command conventions. For example, options are specified with a '-' e.g. "program -format 2".
If in doubt, type:

programname -help

to get some help on the options or

programname -opt

to force the application to prompt you for values for all available options, including ones which are not normally prompted for and for which default values are used. Or

tfm programname

to get the full help on a program

Documentation:
The EMBOSS versions of the latest PHYLIP programs (version 3.x) begin with 'f' to distinguish them from the previous PHYLIP release (version 2.x). e.x. econsense at PHYLOGENY CONSENSUS should be fconsense.
Command is locate at /usr/local/emboss/fconsense
Details please refer to http://emboss.sourceforge.net

Installation:

Source code downloaded from http://emboss.sourceforge.net/download/
Compiled by gcc

System(s): Unix

inQuiry: not available at inQuiry

pcluster: Not available on pcluster

rcluster, IOB : running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster, IOB

Running the various applications by type the application name, i.e.

bsub -q queueName emma

to start multiple alignment program.

The EMBOSS command syntax follows normal UNIX command conventions. For example, options are specified with a '-' e.g. "program -format 2".
If in doubt, type:

programname -help

to get some help on the options or

programname -opt

to force the application to prompt you for values for all available options, including ones which are not normally prompted for and for which default values are used. Or

tfm programname

to get the full help on a program

To run interactive applications, use inter1 node, also refer to running interactive jobs at rcluster, IOB

[username@rcluster ~]$ ssh inter1
[username@inter1 ~]$

To exit interactive node

[username@inter1 ~]$ exit
[username@rcluster ~]$

Documentation: Same as altix

Installation: Same as altix

System(s): Unix