Biotechnology:
Bioinformatics Software
Sites:
- EMBOSS *Cool Site*
- The European Molecular
Biology Open Software Suite.
An open source project started
by the EMBnet community
in order to replace proprieatry
systems like GCG.
- AbOrygen
: Intuitive bioinformatics
- 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 - Freeware DNA
cloning, analysis and visualization
software.
- AnnHyb - Nucleotidic Sequence Manager - 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.
- The
ARB Project - A free
sequence database application
for Unix. It includes a
sequence editor, several
sequence aligners, phylogeny
reconstruction tools, probe/primer
search and generation, genome
annotation and visualization.
In addition to the integrated
user-interface the ARB database
can be accessed using Perl
or C.
- ARCiB
-- Accessible Retired Computers
in Biology - 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 - Bioinformatics programs, including
MendelBase.
- Artemis: A DNA Sequence Viewer and Annotation Tool
- Java program to display
a DNA sequence, annotated
with features, ORFs. Reads
many input formats.
- Bio Informatic Bacterial Identification - Bibliographic
site for management and
alignment of bacteria and
fungi sequences.
- BSML
- Bioinformation Sequence
Markup Language - Extensible
language specification and
container for bioinformatic
data.
- Computer
Program for Polyphasic Taxonomy
Analysis - 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 - An interactive tool for peptide and nucleotide
sequence analysis
- DNA-Star
- Lasergene - Commercial
sequence analysis and manipulation
suite for Windows and Macintosh.
- GDE for Linux - 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
- Normalization tests for
differentially expressed
genes, clustering, bootstrapping,
leave-one-out validation,
cross-fold validation, and
links to external genomic
databases.
- GeneRunner
for Windows - A fairly
old sequence analysis tool
for everyday lab use. Formerly
a commercial product - now
"abandonware."
- GeneticXchange - Software for life science discovery;
enterprise-level data integration
and desktop biologists.
- Gints
- 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
- Sean Eddy's tools to build
HMMs from multiple alignments,
align sequences to HMMs,
calculate e-scores, and
other tools
- JAligner - Java implementation of the dynamic
programming algorithm Smith-Waterman
for biological local pairwise
sequence alignment.
- limmaGUI - A graphical user interface for linear
modelling of cDNA and oligonucleotide
microarray data to identify
differentially expressed
genes.
- Logical
Depth - Accelerated
sequence analysis tools
for HMMsearch and Smith-Waterman.
- LucID
Professional - Software
for creating interactive
keys for biology, taxonomy,
medicine, and agriculture.
- Metalifesocieties - Makes available various bioinformatics
algorithms, which perform
all essential tasks in sequence
analysis and sequence-based
predictions.
- Meta-MEME
v2.0.1 - Software toolkit
for building and using motif-based
hidden Markov models of
DNA and proteins - from
the Univ. of California-San
Diego.
- Molecular
Evolutionary Genetics Analysis
(MEGA2) software - Provides
free downloadable MEGA2
software for use in comparative
sequence analysis of genetic
data. Program for Win32
platforms.
- NCBI BLAST - BLAST (Basic Local Alignment Search
Tool) is a set of similarity
search programs designed
to explore all of the available
sequence databases regardless
of whether the query is
protein or DNA.
- PHRED - Base-Calling Software with Quality Information
- A widely-used program
for calling DNA sequence
bases from sequencer trace
files.
- Phred/Phrap/Consed System Home Page - basecaller
/ assembler / sequencer
finisher and related tools
from the UW Genome Center.
- Premier
Biosoft International
- Developers of software
for real time PCR primer
design, TaqMan, molecular
beacons, DNA microarray
analysis, drawing restriction
plasmid maps, gateway cloning
experiments, protein interaction
network and functional genomics.
- PubCrawler
- An Update Alerting Service
for PubMed and GenBank
- Software and an online
service for periodically
performing predefined searches
at NCBI, reporting new results
by email or on the web.
- The
Sanger Centre: Software
- Production software used
at the Sanger Centre, physical
mapping software, informatics
and analysis software, and
data formats
- Sequence
Analysis for Mac OS X
- A freeware Mac OS X application
written in Java that does
many standard types of DNA
and protein sequence analysis
tasks.
- Sight - Extendable parallel system for automatic
genome analysis. Software
for analysing all potential
genes in a defined genome
region. Given two marker
names, can output reports
of genomic features between
them. Features for converting
between naming systems,
sequence retrieval, E-PCR,
gene prediction, similarity
search, protein pattern
search, and report formatting.
Written in Java.
- Software for Statistical Folding and Rational Design
of Nucleic Acids - Sfold
predicts probable RNA secondary
structures, assesses target
accessibility, and provides
tools for the rational design
of RNA-targeting nucleic
acids. The web server version
is free for academic use.
- STRING - Search for Tandem Repeats IN Genomes
-- Includes C source code
and examples.
- Verbumculus Genetic Sequence Analyzer - An interesting
tool to discover and visualize
over- or under-represented
words in genetic sequences.
Executable for Sparc-Solaris,
Sparc-Intel or Linux-Intel.
Also available as a Java
applet.
- WU-BLAST
Archives - WU-BLAST:
The Washington University
BLAST. "...faster at any
sensitivity, more sensitive
at any speed, the first
BLAST with gapped alignments
and statistics."
- XDigitize - A visualization software system for
evaluation of hybridisation
experiments.
- Linux Software Encyclopedia - Bioinformatics -
Links to Bioinformatics
software for Linux. From
the Linux Software Encyclopedia.
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