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Applications inside bioknoppix

All applications in Bio-Knoppix are open-source.

Application Description Documentation
EMBOSS EMBOSS is a suite where you will find around 100 programs (applications).These are just some of the areas covered:
  • 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

Jemboss Jemboss is a java based interface to EMBOSS. It provides the advantage of being able to provide sensible EMBOSS defaults on-the-fly for a given sequence or for a given input parameter. Jemboss can run the EMBOSS applications interactively or as a batch process. The progress of the batch processes are monitored by a job manager.

Artemis Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.

ClustalX Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen.

Cn3D Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.
ImageJ ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

BioPython The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics

Rasmol RasMol is a free program which displays molecular structure.

Bioperl Bioperl is a tookit of perl modules useful in building bioinformatics solutions in perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.
Bioconductor Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data (bioinformatics).

Created by carlos_zope
Last modified 2004-06-23 03:17 PM
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