Software: Bioinformatics

 
CLC Sequence Viewer 6.6CLC bio A/S

CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses.CLC Sequence Viewer is very versatile when it comes to importing and exporting both data and graphics files.The application has smooth data management,excellent graphical viewing and output options.

Platform: WindowsGraphic Apps- Editors
License: FreewareSize: 41.1 MBReleased: 13 May, 2012
Download: http://download.clcbio.com//CLCSequenceViewer/6.6.1/CLCSequenceViewer_6_6_1.exe
Avogadro 1.0.3dcurtis3

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.

Features:

* Cross-Platform: Molecular builder for Windows, Linux, and Mac

Avogadro 1.0.3 by dcurtis3
Platform: WindowsGraphic Apps- Editors
License: FreewareSize: 9.7 MBReleased: 18 March, 2012
Download: http://sourceforge.net/projects/avogadro/files/avogadro/1.0.3/Avogadro-1.0.3-win32.exe/download?use_mirror=voxel
STRAP- Multiple Protein Alignments 6.8Christoph Gille Charite, Institute for Biochemistry

With this free Java software you can:
- Use latest bioinformatics tools with an intuitive user interface
- Compare proteins by sequence and 3D-similarity
- Search protein databases
- Publish protein alignments online
- Use STRAP to view results of bioinformatics services

Platform: WindowsHome & Hobby- Health & Nutrition
License: FreewareSize: 3.3 MBReleased: 14 June, 2012
Download: http://www.bioinformatics.org/strap/install2/strap-windows.zip
Mussagl 1.1Wold Lab - Caltech

Mussa is a bioinformatics tool for finding and visualizing regions of conserved DNA by comparing across several species. It has been found that conserved regions are frequently enriched for regions that are functionally important. Thus Mussa is a tool to help discover previously unknown functional DNA elements.

Platform: WindowsNetwork & Internet- Other
License: FreewareSize: 12.6 MBReleased: 30 June, 2012
Download: http://woldlab.caltech.edu/~king/mussagl/releases/mussa-v1_1_0-b20091123-win32-setup.exe
Cytoscape 2.8Cytoscape Consortium

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Although Cytoscape was originally designed for biological research, now it is a general platform for complex network ...

Platform: WindowsBusiness- Math & Scientific Tools
License: FreewareSize: 87.2 MBReleased: 28 May, 2012
Download: http://www.cytoscape.org/download.html
GATCViewer 1.0GATC Biotech AG


DNA sequencing service, Next Generation sequencing, bioinformatics services and sequencing analysis software.European leaders in DNA sequencing and bioinformatics

Platform: WindowsBusiness- Other
License: FreewareSize: 1.8 MBReleased: 01 July, 2012
Download: http://www.gatc-biotech.com/en/textbausteine/downloadsundntzlichelinks.html
BioPathXplore 1.0biopathxplore.sourceforge.net

BioPathXplore is a Bioinformatics Pathway eXploration tool for the visualization and exploration of biological pathways through the integration of KEGG pathways and high throughput data, using Petri nets. View and analyze biological pathways with this tool.BioPathXplore Features:
1. Visualization of KEGG Pathways
2. Integration of High Throughput ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 21.6 MBReleased: 19 April, 2013
Download: http://biopathxplore.sourceforge.net
Genome Explorer 1.0cbr.jic.ac.uk

Genome Explorer offer users a single interface for some useful bioinformatics tools.
It provides additional functionality for searching sequence data (for particular groups of nucleotides or amino acids) and editing multiple sequence alignments.Requirements:
* Java

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 2.5 MBReleased: 01 April, 2013
Download: http://cbr.jic.ac.uk
Bioinformatics - Computational Biology - Computational - Analysis
Geneious Basic x64 5. 5. 2004Biomatters Ltd



Geneious is a cross-platform research engine for the retrieval, organization and analysis of biomolecular data that allows any molecular biologist do core bioinformatics tasks in a flash by removing painful data-administration.

Geneious comes pre-bundled with bioinformatics functions from publication or nucleotide searching ...

Geneious Basic x64 5. 5. 2004 by Biomatters Ltd
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 39.6 MBReleased: 06 May, 2012
Download: http://www.geneious.com/assets/installers/geneious/release/Geneious_win64_5_5_4_with_jre.exe
Cn3D 4.3NCBI



Cn3D is a utility for professional specialists in the genetics and bioinformatics fields who access the NCBI online database and need to view the 3D structures of bio-molecules and to see their correlation with amino-acid sequences.

Platform: WindowsNetwork & Internet- Browser Tools
License: FreewareSize: 0Released: 13 March, 2012
Download: http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
DAMBE 5.2Xuhua Xia


Features:
Sequence alignment
¨ General sequence alignment with nucleotide and amino acid sequences
¨ Aligning protein-coding nucleotide sequences against aligned amino acid sequences


Bioinformatics tools
¨ Position weight matrix for characterizing and predicting sequence motifs

Platform: WindowsEducation- Other
License: FreewareSize: 9.4 MBReleased: 13 April, 2012
Download: http://dambe.bio.uottawa.ca/download/DAMBEXP.msi
GenGIS 1.0Robert Beiko

GenGIS is a bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy ...

Platform: WindowsGraphic Apps- Other
License: FreewareSize: 26.2 MBReleased: 24 February, 2012
Download: http://kiwi.cs.dal.ca/~beiko/MediaWiki/mediawiki-1.13.4/images/e/ef/GenGIS_v1.08_Windows.zip
PAICE 2.90paice.sourceforge.net

PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.Requirements:
* Java

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 2.7 MBReleased: 01 January, 2013
Download: http://paice.sourceforge.net
DAMBE (Data Analysis and Molecular Biology and Evolution) 5.2.30dambe.bio.uottawa.ca

Bioinformatics tools
* Position weight matrix for characterizing and predicting sequence motifs
* Perceptron for two-group classification of sequence motifs
* Gibbs sampler for characterizing and predicting novel/hidden sequence motifs
* Hidden Markov models
* Secondary structure prediction
* tRNA anticodon identification

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 10.1 MBReleased: 28 March, 2013
Download: http://dambe.bio.uottawa.ca
PAUP - PHYLIP - Mega - Beast
GNLab (Gene Network virtual Laboratory) 1.0www.it.usyd.edu.au

GNLab (Gene Network virtual Laboratory) is a novel bioinformatics tool for the large-scale analysis of gene regulatory networks (GRNs). This C++ command-line tool supports the analysis of both the static structure and dynamic behaviour of a GRN. GNLab is developed to support the design and implementation of large-scale repeatable computational experimentations ...

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 673.2 KBReleased: 08 March, 2013
Download: http://sydney.edu.au/engineering/it/
Information Systems - Computer Science - Information Technology - Information Technologies
TASE: Illumina Solexa annotation 1.5.1tase.sourceforge.net

A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with any CASAVA build, providing annotation, tag counts and visualization in a rapid manner.Requirements:
* Java

Platform: WindowsBusiness- Calculators & Converters
License: FreewareSize: 3.5 MBReleased: 21 March, 2013
Download: http://tase.sourceforge.net
USeq 7. 8. 2006Robb Cundick&David Nix



USeq is under continuous development at the Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.
A description of the statistics and comparison of methods used in USeq is now published, see Nix DA, Courdy SJ, Boucher KM: Empirical methods for controlling false positives and estimating confidence in chIP-seq ...

Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 7.6 MBReleased: 17 April, 2012
Download: http://sourceforge.net/projects/useq/files/USeq_7.8.6.zip/download
AltAnalyze for Linux 2.02 Beta Nathan Salomonis & Bruce Conklin

This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction read or microarray files along with some simple descriptions of the conditions that you're analyzing. RNASeq support is introduced in AltAnalyze 2.0.

AltAnalyze for Linux 2.02 Beta  by Nathan Salomonis & Bruce Conklin
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 39.5 MBReleased: 16 May, 2012
Download: http://code.google.com/p/altanalyze/
AltAnalyze for Mac OS X 2.02 Beta Nathan Salomonis & Bruce Conklin

This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction read or microarray files along with some simple descriptions of the conditions that you're analyzing. RNASeq support is introduced in AltAnalyze 2.0.

AltAnalyze for Mac OS X 2.02 Beta  by Nathan Salomonis & Bruce Conklin
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 27.2 MBReleased: 24 February, 2012
Download: http://code.google.com/p/altanalyze/
AltAnalyze x64 2.02 Beta Nathan Salomonis & Bruce Conklin

This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction read or microarray files along with some simple descriptions of the conditions that you're analyzing. RNASeq support is introduced in AltAnalyze 2.0.

AltAnalyze x64 2.02 Beta  by Nathan Salomonis & Bruce Conklin
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 42.4 MBReleased: 04 February, 2012
Download: http://code.google.com/p/altanalyze/
AltAnalyze 2.02 Beta Nathan Salomonis & Bruce Conklin

This software requires no advanced knowledge of bioinformatics programs or scripting. All you will need are your junction read or microarray files along with some simple descriptions of the conditions that you're analyzing. RNASeq support is introduced in AltAnalyze 2.0.

AltAnalyze 2.02 Beta  by Nathan Salomonis & Bruce Conklin
Platform: WindowsGraphic Apps- CAD
License: FreewareSize: 42.4 MBReleased: 29 June, 2012
Download: http://code.google.com/p/altanalyze/
BlastViewer 2 2korilog.com

BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the NCBI and the EBI BLAST sequence database search systems.

Platform: WindowsHome & Hobby- Other
License: FreewareSize: 5.4 MBReleased: 13 February, 2012
Download: http://www.korilog.com/products/BlastViewer-2.3.exe
pIcarver 3.1Proteome Informatics Group (Swiss Institute of Bioinformatics)

This tool has been developed as a service of the Bioinformatics Core Facility, within a collaboration between the Proteome Informatics Group from the Swiss Institute of Bioinformatics (SIB) and the Biomedical Proteomics Research Group

Platform: WindowsHome & Hobby- Other
License: FreewareSize: 1.3 KBReleased: 06 June, 2012
Download: http://web.expasy.org/picarver/
Mascot Daemon 2.3Matrix Science

Mascot Daemon is a client application which automates the submission of data files to Mascot server. It runs under Microsoft Windows 2000, XP, Server 2003, Vista, Server 2008, and 7.

Multiple Daemon clients can submit searches to a single Mascot server. If you have several mass spectrometers, you can install separate copies of Daemon on ...

Platform: WindowsHome & Hobby- Personal Interest
License: FreewareSize: 585.5 KBReleased: 03 February, 2012
Download: http://www.matrixscience.com/patches/MascotDaemon_20100721.exe
REST 2008 2.0gene quantification

REST 2008 is a standalone software package for analyzing gene expression using real-time amplification data. The software addresses issues surrounding the measurement of uncertainty in expression ratios by introducing randomization and bootstrapping techniques. New confidence intervals for expression levels also allow measurement of not only the statistical ...

Platform: WindowsHome & Hobby- Personal Interest
License: FreewareSize: 70.5 MBReleased: 08 February, 2012
Download: http://www.gene-quantification.de/rest-2008.html
BioLign 4.0Tom Hall

BioLign is a multiple contig alignment editor which constructs multiple alignments from the output generated. It allows integrated and synchronized viewing and unrestricted editing of both the base calls of the contig and the alignment itself.
This is a great tool for alignment, SNP identification, and PHRAP evaluation.

Platform: WindowsSystem Utilities- Other
License: FreewareSize: 4.0 MBReleased: 21 June, 2012
Download: http://www.maizegenetics.net/images/stories/bioinformatics/biolign/biolign.zip
Seqtools 8.4Soeren W. Rasmussen

SEQtools - a program suite for sequence analysis
Seqtools is a large collection of tools for basic and advanced analyses of nucleotide and protein sequences. The tools are wrapped into a common user interface making handling, storage, retrieval and viewing the results easy and logical.

Platform: WindowsWeb Development- Web Other
License: FreewareSize: 11.3 MBReleased: 12 March, 2012
Download: http://www.seqtools.dk/st8download/seqtools84.msi
Ontologizer 6.0Ontologizer Open Source Team

Following analysis with one of the above methods and optionally a multiple-testing correction procedure, the Ontologizer rows of terms together with their p-values or marginal probabilities, annotation counts and other information.

Relevance of a term is indicated by color coding according to the sub ontology to which the term belongs, ...

Platform: WindowsBusiness- Other
License: FreewareSize: 1.2 KBReleased: 13 June, 2012
Download: http://compbio.charite.de/index.php/ontologizer2.html
QTAntimony 2.1 betaLucian Smith

For more information and to reference Antimony, see our article in Bioinformatics. If this page doesn't link to what you need, try the sourceforge default Antimony project page

Platform: WindowsBusiness- Other
License: FreewareSize: 5.6 MBReleased: 24 February, 2012
Download: http://sourceforge.net/projects/antimony/files/Windows%20binaries/2.1-beta/antimonyInstaller_v2.1.0-beta.exe/download?use_mirror=iweb
BioDesk 6.5BioEnable Technologies Pvt Ltd

BioDesk is a desktop application that provides a convenient menu-driven interface to the BCF UNIX servers. The menu allows you to launch a variety of Life Sciences applications and XTerminal windows for running command line applications. BioDesk also allows the BCF staff to remotely connect to your session to assist you. For more detailed information, ...

Platform: WindowsDesktop- Other
License: FreewareSize: 496.1 KBReleased: 10 March, 2012
Download: http://bcf.arl.arizona.edu/resources/software/biodesk/biodesk.exe


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