Genomics software

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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.
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