Difference between revisions of "Genomics software"
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</font>See also: [http://biosoftware.org Biosoftware.org]<br /> | </font>See also: [http://biosoftware.org Biosoftware.org]<br /> | ||
</strong><br /> | </strong><br /> | ||
| − | <table | + | <table height="1653" width="100%" cellspacing="0" cellpadding="0" border="1" summary="" style="background-color: rgb(255, 255, 255);"> |
<tbody> | <tbody> | ||
<tr> | <tr> | ||
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<td><a href="http://www.bioexplorer.net/toolbar/"><font color="#810081">Bioexplorer Toolbar</font></a></td> | <td><a href="http://www.bioexplorer.net/toolbar/"><font color="#810081">Bioexplorer Toolbar</font></a></td> | ||
<td> An easy toolbar for NCBI databases</td> | <td> An easy toolbar for NCBI databases</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>[[BioJava]]</td> | ||
| + | <td> Biological module for Java programming language.</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 27: | Line 31: | ||
<tr> | <tr> | ||
<td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm"><font color="#810081">Biotech Resource</font></a><font color="#c0c0c0"> at UNM.edu</font></td> | <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm"><font color="#810081">Biotech Resource</font></a><font color="#c0c0c0"> at UNM.edu</font></td> | ||
| − | <td> <font color="#000000 | + | <td> <font size="2" color="#000000">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></td> |
| + | </tr> | ||
| + | <tr> | ||
| + | <td>[[BioPerl]]</td> | ||
| + | <td> BioPerl: biological module for Perl programming language.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>[[BioPHP]]</td> | ||
| + | <td> BioPHP: biological module for PHP programming language.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>[[BioPython]]</td> | ||
| + | <td> BioPython: biological module for Python programming language.</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>[[BioRuby]]</td> | ||
| + | <td> BioRuby: biological module for Ruby programming language</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
| Line 39: | Line 59: | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
| − | <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 | ||
| − | |||
</tr> | </tr> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
| − | <td><a | + | <td><a href="http://www.psc.edu/biomed/genedoc/" target="new"><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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
| − | <td><a title="Enhanced with automated teaching methods, MassARRAY RT software automatically aligns and calibrates SEQUENOM's SpectroCHIP and provides smart rastering of DNA samples in real time without user intervention. Smart rastering dramatically improves sample efficiency and reduces individual analysis times for improved data quality and sample throughput. | + | <td><a href="http://www.sequenom.com/genetic_systems/software/software_rt.php" title="Enhanced with automated teaching methods, MassARRAY RT software automatically aligns and calibrates SEQUENOM's SpectroCHIP and provides smart rastering of DNA samples in real time without user intervention. Smart rastering dramatically improves sample efficiency and reduces individual analysis times for improved data quality and sample throughput."><font size="-1">MassARRAY™ RT Software (Sequenom)</font></a> </td> |
<td> </td> | <td> </td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><font color="#000000"><a | + | <td><font color="#000000"><a href="http://www.gsf.de/biodv/matinspector.html" target="new">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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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> | ||
<tr> | <tr> | ||
<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=" | + | <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=" | ||
| − | |||
</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=" | + | <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=" | ||
</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 | + | <td><font color="#000000"><a href="http://compbio.ornl.gov/structure/prospect/" target="new">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> | ||
<tr> | <tr> | ||
| − | <td><font color="#000000"><a | + | <td><font color="#000000"><a href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html" target="new">TreeView</a></font></td> |
<td><font color="#000000">Tree drawing software for Apple Macintosh and Windows</font></td> | <td><font color="#000000">Tree drawing software for Apple Macintosh and Windows</font></td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<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>[http://gi.biotec.or.th/resources/vartree VarTree]</td> |
| − | <td>Washington | + | <td> A Decision Tree Based Tool for Analyzing Gene-Gene Interaction</td> |
| + | </tr> | ||
| + | <tr> | ||
| + | <td><a href="http://blast.wustl.edu/">WU-BLAST</a> </td> | ||
| + | <td> Washington University BLAST archives</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>[http://ugene.unipro.ru UGENE]<br /> | ||
| + | </td> | ||
| + | <td>Integrated visual environment for popular command line bioinformatics tools like HMMER, MUSCLE, BLAST, repeats and restriction enzymes analysis etc.</td> | ||
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
Latest revision as of 21:00, 13 February 2009
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. |
