Genomics software
Revision as of 20:58, 13 February 2009 by imported>Mfursov (a link to UGENE software tool was added)
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 |
| Unipro UGENE | Integrated visual environment for popular command line bioinformatics tools like HMMER, MUSCLE, BLAST, repeats and restriction enzymes analysis etc. |