a Genomics, Proteomics and Bioinformatics Knowledge Base
123 Genomics - programming info for bioperl, biopython, biojava, bioxml; free analysis softwares; major analysis servers

Free Softwares
Alscript Program to format multiple sequence alignments
Amplify Macintosh program for simulating and testing PCRs
Biocatalogue Software directory of general interest in molecular biology and genetics, at EBI
Bioexplorer Toolbar Fastest and easiest way to get the information you want from NCBI databases
Biostatistics Biostatistics software
Biotech Resource Free softwares for moleular biology and structural biology
BLAST at NCBI Blast open source software
Cn3D Application that allows to view 3D structures, at NCBI
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 sequence analysis
eXtropia Several free web tools
Fasta Open source for Fasta
Genamics Database of freely-distributable and commercial tools for use in molecular biology
GeneDoc Multiple sequence alignment editor, analyzer & shading utility for windows
Globin Several free tools
GNU Free software foundation - several tools
HMMER HMMER 2.2 Profile hidden Markov models for biological sequence analysis 
NIH Image Image analysis program for Macintosh from NIH
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
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
WU-BLAST Washington university BLAST archives
BioPAX Develop a common exchange format for biological pathways data.
Genesis Information about GEneral NEural SImulation System
E-cell Simulating intracellular molecular processes of living cells project
CodeBits.com Find building blocks for your programming needs in many languages
ItKnowledge Read or search the full-text of technical and computer books, tutorials and guides
Programming Libraries Bioinformatics Programming Libraries, links to lots of sites and source odes
Banbury Gene identification software benchmarking site
BIONLP.org Natural language processing of biology text
Global Grid Forum Distributed computing
Linux.org Linux is a free Unix-type operating system
Linux BC Linux user group in British Columbia
Icon Bank Icon, button, background or line to spice up your website
NodalPoint Culture, molecular biology, biotechnology, linux and bioinformatics news
SBML The systems biology markup language
WinFiles Lots of windows related information from CNET

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