Difference between revisions of "Genomics software"
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<td><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/">BLAST at NCBI</a></td> | <td><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/">BLAST at NCBI</a></td> | ||
| − | <td>Blast | + | <td> Blast [[public domain]] software served by NCBI of USA.</td> |
</tr> | </tr> | ||
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<td><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a></td> | <td><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a></td> | ||
| − | <td>Application that allows to view 3D structures, at NCBI</td> | + | <td> Application that allows to view 3D structures, at NCBI, NIH, USA.</td> |
</tr> | </tr> | ||
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| − | <td valign="top"><a href="http://www.clcbio.com/index.php?area=software&section=free">CLC Bio</a> | + | <td valign="top"><a href="http://www.clcbio.com/index.php?area=software&section=free">CLC Bio</a></td> |
| − | + | <td valign="top"> Basic bioinformatics analyses and data management - free download</td> | |
| − | <td valign="top">Basic bioinformatics analyses and data management - free download | ||
| − | |||
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<td><font color="#000000"><a href="http://compbio.ornl.gov/structure/domainparser/">DomainParser</a></font></td> | <td><font color="#000000"><a href="http://compbio.ornl.gov/structure/domainparser/">DomainParser</a></font></td> | ||
| − | <td><font color="#000000">A protein domain partition program</font></td> | + | <td><font color="#000000"> A protein domain partition program</font></td> |
</tr> | </tr> | ||
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<td><a href="http://www.emboss.org/">EMBOSS</a></td> | <td><a href="http://www.emboss.org/">EMBOSS</a></td> | ||
| − | <td>EMBOSS is a package of | + | <td> EMBOSS is a package of free open source software for bioinformatic analyses</td> |
</tr> | </tr> | ||
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<td><a href="http://www.e-cell.org/">E-cell</a></td> | <td><a href="http://www.e-cell.org/">E-cell</a></td> | ||
| − | <td>Simulating intracellular molecular processes of living cells project</td> | + | <td> Simulating intracellular molecular processes of living cells project</td> |
</tr> | </tr> | ||
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<td><a href="http://www.extropia.com/applications.html">eXtropia</a></td> | <td><a href="http://www.extropia.com/applications.html">eXtropia</a></td> | ||
| − | <td>Several free web tools</td> | + | <td> Several free web tools</td> |
</tr> | </tr> | ||
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<td><a href="ftp://ftp.virginia.edu/pub/fasta/">Fasta</a></td> | <td><a href="ftp://ftp.virginia.edu/pub/fasta/">Fasta</a></td> | ||
| − | <td>Open source for Fasta</td> | + | <td> Open source for Fasta</td> |
</tr> | </tr> | ||
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<td><a href="http://genamics.com/software/"><font color="#810081">Genamics</font></a></td> | <td><a href="http://genamics.com/software/"><font color="#810081">Genamics</font></a></td> | ||
| − | <td>Gen<font color="#ff0000">a</font>mics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry</td> | + | <td> Gen<font color="#ff0000">a</font>mics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry</td> |
</tr> | </tr> | ||
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<td><a target="new" href="http://www.psc.edu/biomed/genedoc/"><font color="#810081">GeneDoc</font></a></td> | <td><a target="new" href="http://www.psc.edu/biomed/genedoc/"><font color="#810081">GeneDoc</font></a></td> | ||
| − | <td><font color="#000000">Multiple sequence alignment editor, analyzer & shading utility for windows</font></td> | + | <td><font color="#000000"> Multiple sequence alignment editor, analyzer & shading utility for windows</font></td> |
</tr> | </tr> | ||
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<td><a href="http://genesis.bbb.caltech.edu/GENESIS/genesis.html">Genesis</a></td> | <td><a href="http://genesis.bbb.caltech.edu/GENESIS/genesis.html">Genesis</a></td> | ||
| − | <td>Information about GEneral NEural SImulation System</td> | + | <td> Information about GEneral NEural SImulation System</td> |
</tr> | </tr> | ||
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<td><a href="http://globin.cse.psu.edu/">Globin</a></td> | <td><a href="http://globin.cse.psu.edu/">Globin</a></td> | ||
| − | <td>Several free tools</td> | + | <td> Several free tools</td> |
</tr> | </tr> | ||
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<td><a href="http://www.gnu.org/">GNU</a></td> | <td><a href="http://www.gnu.org/">GNU</a></td> | ||
| − | <td>Free software foundation - several tools</td> | + | <td> Free software foundation - several opensource programming tools for free OS such as [[LINUX]].</td> |
</tr> | </tr> | ||
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<td><a href="http://hmmer.wustl.edu/">HMMER</a></td> | <td><a href="http://hmmer.wustl.edu/">HMMER</a></td> | ||
| − | <td>HMMER | + | <td> HMMER: Hidden Markov models for biological sequence analysis by Sean Eddy. </td> |
</tr> | </tr> | ||
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<td><a href="http://rsb.info.nih.gov/nih-image/">NIH Image</a></td> | <td><a href="http://rsb.info.nih.gov/nih-image/">NIH Image</a></td> | ||
| − | <td>Image analysis program for Macintosh from NIH</td> | + | <td> Image analysis program for Macintosh from NIH</td> |
</tr> | </tr> | ||
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<td><font color="#000000"><a target="new" href="http://www.gsf.de/biodv/matinspector.html">MatInspector</a></font></td> | <td><font color="#000000"><a target="new" href="http://www.gsf.de/biodv/matinspector.html">MatInspector</a></font></td> | ||
| − | <td><font color="#000000">Detection of transcription factor binding sites</font></td> | + | <td><font color="#000000"> Detection of transcription factor binding sites</font></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.scriptarchive.com/">Matt's Script Archive</a></td> | <td><a href="http://www.scriptarchive.com/">Matt's Script Archive</a></td> | ||
| − | <td>Several free Perl scripts</td> | + | <td> Several free Perl scripts</td> |
</tr> | </tr> | ||
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<td><a href="http://www.mbshortcuts.com/software/index.htm">MB Shotcuts</a></td> | <td><a href="http://www.mbshortcuts.com/software/index.htm">MB Shotcuts</a></td> | ||
| − | <td>List of several free molecular biology softwares</td> | + | <td> List of several free molecular biology softwares</td> |
</tr> | </tr> | ||
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<td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm"><font color="#810081">MolBio Links</font></a></td> | <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm"><font color="#810081">MolBio Links</font></a></td> | ||
| − | <td>Links to several molecular biology toos</td> | + | <td> Links to several molecular biology toos</td> |
</tr> | </tr> | ||
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<td><font color="#000000"><a href="http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/Listings.html">Molecular Biology</a></font></td> | <td><font color="#000000"><a href="http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/Listings.html">Molecular Biology</a></font></td> | ||
| − | <td>List of many free software package for Mac and PC</td> | + | <td> List of many free software package for Mac and PC</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><font color="#000000"><a href="http://theory.lcs.mit.edu/~elwolf/multicoil.html">Multicoil</a></font></td> | <td><font color="#000000"><a href="http://theory.lcs.mit.edu/~elwolf/multicoil.html">Multicoil</a></font></td> | ||
| − | <td><font color="#000000">Program to p</font>redict coiled coil regions in proteins</td> | + | <td><font color="#000000"> Program to p</font>redict coiled coil regions in proteins</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td style="VERTICAL-ALIGN: top"><a href="http://www.drive5.com/muscle/">MUSCLE</a> | + | <td style="VERTICAL-ALIGN: top"><a href="http://www.drive5.com/muscle/">MUSCLE</a></td> |
| − | + | <td style="VERTICAL-ALIGN: top"> Protein Multiple Sequence Alignment Software</td> | |
| − | <td style="VERTICAL-ALIGN: top">Protein Multiple Sequence Alignment Software | ||
| − | |||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td valign="top"><a href="http://www.softgenetics.com/">MutationSurveyor</a><a href="http://www.softgenetics.com/"> & MutationExplorer</a></td> | <td valign="top"><a href="http://www.softgenetics.com/">MutationSurveyor</a><a href="http://www.softgenetics.com/"> & MutationExplorer</a></td> | ||
| − | <td valign="top">Analysis of DNA variants, SNPs and mutations | + | <td valign="top"> Analysis of DNA variants, SNPs and mutations</td> |
| − | |||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.openinformatics.org/">Open Informatics</a></td> | <td><a href="http://www.openinformatics.org/">Open Informatics</a></td> | ||
| − | <td>Open source softwares</td> | + | <td> Open source softwares</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.phrap.org/">Phred, Phrap & Consed</a></td> | <td><a href="http://www.phrap.org/">Phred, Phrap & Consed</a></td> | ||
| − | <td>Sequence quality and assembly softwares</td> | + | <td> Sequence quality and assembly softwares</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td style="VERTICAL-ALIGN: top"><a href="http://chum.gs.washington.edu/PolyPhred.html">PolyPhred</a> | + | <td style="VERTICAL-ALIGN: top"><a href="http://chum.gs.washington.edu/PolyPhred.html">PolyPhred</a></td> |
| − | + | <td style="VERTICAL-ALIGN: top"> Compares traces to identify heterozygous sites for SNPs</td> | |
| − | <td style="VERTICAL-ALIGN: top">Compares traces to identify heterozygous sites for SNPs</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td valign="top"><a href="http://physionet.org/">PhysioNet</a> | + | <td valign="top"><a href="http://physionet.org/">PhysioNet</a></td> |
| − | + | <td valign="top"> Collection of physiologic simulation software</td> | |
| − | <td valign="top">Collection of physiologic simulation software | ||
| − | |||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><font color="#000000"><a href="http://www.chemicalgraphics.com/">PovChem</a></font></td> | <td><font color="#000000"><a href="http://www.chemicalgraphics.com/">PovChem</a></font></td> | ||
| − | <td><font color="#000000">Visualization program for PDB protein structures</font></td> | + | <td><font color="#000000"> Visualization program for PDB protein structures</font></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.hgmp.mrc.ac.uk/CCP11/code_libraries.txt.html#21">Programming Libraries</a></td> | <td><a href="http://www.hgmp.mrc.ac.uk/CCP11/code_libraries.txt.html#21">Programming Libraries</a></td> | ||
| − | <td>Bioinformatics Programming Libraries, links to lots of sites and source codes</td> | + | <td> Bioinformatics Programming Libraries, links to lots of sites and source codes</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><font color="#000000"><a target="new" href="http://compbio.ornl.gov/structure/prospect/">Prospect</a></font></td> | <td><font color="#000000"><a target="new" href="http://compbio.ornl.gov/structure/prospect/">Prospect</a></font></td> | ||
| − | <td><font color="#000000">A threading-based protein structure prediction system</font></td> | + | <td><font color="#000000"> A threading-based protein structure prediction system</font></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://lib.stat.cmu.edu/R/CRAN/">R - statistical package</a></td> | <td><a href="http://lib.stat.cmu.edu/R/CRAN/">R - statistical package</a></td> | ||
| − | <td>Statistical computing and graphics software</td> | + | <td> Statistical computing and graphics software</td> |
</tr> | </tr> | ||
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<td><a href="http://sourceforge.net/softwaremap/trove_list.php?form_cat=252">SourceForge.net</a></td> | <td><a href="http://sourceforge.net/softwaremap/trove_list.php?form_cat=252">SourceForge.net</a></td> | ||
| − | <td>Several ready to use tool</td> | + | <td> Several ready to use tool</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.mrc-lmb.cam.ac.uk/pubseq/">Staden Package</a></td> | <td><a href="http://www.mrc-lmb.cam.ac.uk/pubseq/">Staden Package</a></td> | ||
| − | <td>A excellent package for sequence analysis and assembly</td> | + | <td> A excellent package for sequence analysis and assembly</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.ualberta.ca/~stothard/javascript/d_load.html">Sequence Manipulation</a></td> | <td><a href="http://www.ualberta.ca/~stothard/javascript/d_load.html">Sequence Manipulation</a></td> | ||
| − | <td>Free suite of sequence manipulation tools</td> | + | <td> Free suite of sequence manipulation tools</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><a href="http://blast.wustl.edu/">WU-BLAST</a></td> | + | <td><a href="http://blast.wustl.edu/">WU-BLAST</a> </td> |
| − | <td>Washington | + | <td> Washington University BLAST archives</td> |
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
Revision as of 16:27, 15 January 2008
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 |
| 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 |
| 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 |
| WU-BLAST | Washington University BLAST archives |
