Genomics Software

See also: Biosoftware.org

Alscript by Barton Group	Program to format multiple sequence alignments by Geof Barton group.
Amplify	Amplify is a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs).
Biocatalogue	EBI software directory of general interest in molecular biology and genetics.
Bioexplorer Toolbar	An easy toolbar for NCBI databases
BioJava	Biological module for Java programming language.
BioPAX	Develop a common exchange format for biological pathways data.
Biotech Resource at UNM.edu	Free Software that is Relevant to the Molecular Biology and Structural Biology Fields
BioPerl	BioPerl: biological module for Perl programming language.
BioPHP	BioPHP: biological module for PHP programming language.
BioPython	BioPython: biological module for Python programming language.
BioRuby	BioRuby: biological module for Ruby programming language
BLAST at NCBI	Blast public domain software served by NCBI of USA.
BoxShade	Pretty Printing and Shading of Multiple-Alignment files from www.ch.embnet.org
Cn3D	Application that allows to view 3D structures, at NCBI, NIH, USA.
CLC Bio	Basic bioinformatics analyses and data management - free download
DomainParser	A protein domain partition program
EMBOSS	EMBOSS is a package of free open source software for bioinformatic analyses
E-cell	Simulating intracellular molecular processes of living cells project
eXtropia	Several free web tools
Fasta	Open source for Fasta
Genamics	Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry
GeneDoc	Multiple sequence alignment editor, analyzer & shading utility for windows
Genesis	Information about GEneral NEural SImulation System
Globin	Several free tools
GNU	Free software foundation - several opensource programming tools for free OS such as LINUX.
HMMER	HMMER: Hidden Markov models for biological sequence analysis by Sean Eddy.
NIH Image	Image analysis program for Macintosh from NIH
MassARRAY™ RT Software (Sequenom)
MatInspector	Detection of transcription factor binding sites
Matt's Script Archive	Several free Perl scripts
MB Shotcuts	List of several free molecular biology softwares
MolBio Links	Links to several molecular biology toos
Molecular Biology	List of many free software package for Mac and PC
Multicoil	Program to predict coiled coil regions in proteins
MUSCLE	Protein Multiple Sequence Alignment Software
MutationSurveyor & MutationExplorer	Analysis of DNA variants, SNPs and mutations
Open Informatics	Open source softwares
Phred, Phrap & Consed	Sequence quality and assembly softwares
PolyPhred	Compares traces to identify heterozygous sites for SNPs
PhysioNet	Collection of physiologic simulation software
PovChem	Visualization program for PDB protein structures
Programming Libraries	Bioinformatics Programming Libraries, links to lots of sites and source codes
Prospect	A threading-based protein structure prediction system
R - statistical package	Statistical computing and graphics software
TreeView	Tree drawing software for Apple Macintosh and Windows
SourceForge.net	Several ready to use tool
Staden Package	A excellent package for sequence analysis and assembly
Sequence Manipulation	Free suite of sequence manipulation tools
VarTree	A Decision Tree Based Tool for Analyzing Gene-Gene Interaction
WU-BLAST	Washington University BLAST archives
UGENE	Integrated visual environment for popular command line bioinformatics tools like HMMER, MUSCLE, BLAST, repeats and restriction enzymes analysis etc.