Biology: Bioinformatics: Software

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Software Development (15)

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AbOrygen : Intuitive bioinformatics
http://www.aborygen.com
AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.

AcaClone pDRAW32
http://www.acaclone.com
Freeware DNA cloning, analysis and visualization software.

AnnHyb - Nucleotidic Sequence Manager
http://bioinformatics.org/annhyb/
Free software for working with and managing nucleotide sequences in multiple formats. Many features including sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.

ARCiB -- Accessible Retired Computers in Biology
http://arcib.dowling.edu/
NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.

Array Genetics
http://www.arraygenetics.com/product_overview.php3
Bioinformatics programs, including MendelBase.

Artemis: A DNA Sequence Viewer and Annotation Tool
http://www.sanger.ac.uk/Software/Artemis/
Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.

Bio Informatic Bacterial Identification
http://pbil.univ-lyon1.fr/bibi/query.php
Bibliographic site for management and alignment of bacteria and fungi sequences.

BSML - Bioinformation Sequence Markup Language
http://www.bsml.org/
Extensible language specification and container for bioinformatic data.

Computer Program for Polyphasic Taxonomy Analysis
http://www.proBiosys.com
The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use.

DARWIN
http://cbrg.inf.ethz.ch/Darwin/index.html
An interactive tool for peptide and nucleotide sequence analysis

DNA-Star - Lasergene
http://www.dnastar.com/
Commercial sequence analysis and manipulation suite for Windows and Macintosh.

EMBOSS
http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/
The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.

GDE for Linux
http://www.bioafrica.net/GDElinux/index.html
An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.

Gene Expression Data Analysis web application
http://bioinformatics.upmc.edu/GE2/GEDA.html
Normalization tests for differentially expressed genes, clustering, bootstrapping, leave-one-out validation, cross-fold validation, and links to external genomic databases.

GeneRunner for Windows
http://www.generunner.com
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."

GeneticXchange
http://www.geneticxchange.com/
Software for life science discovery; enterprise-level data integration and desktop biologists.

Gints
http://gints.free.Fr
Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.

HMMER - profile hidden Markov models for sequence analysis
http://hmmer.wustl.edu/
Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools

JAligner
http://jaligner.sourceforge.net/
Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.

limmaGUI
http://bioinf.wehi.edu.au/limmaGUI/index.html
A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.

Linux Software Encyclopedia - Bioinformatics
http://stommel.tamu.edu/~baum/linuxlist/linuxlist/node9.html#biochemistry
Links to Bioinformatics software for Linux. From the Linux Software Encyclopedia.

Logical Depth
http://logicaldepth.com/
Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.

LucID Professional
http://www.lucidcentral.com/
Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.

Meta-MEME v2.0.1
http://metameme.sdsc.edu/
Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.

Metalifesocieties
http://metalifesocieties.tripod.com/
Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.

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