Difference between revisions of "Search for Softwares"
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<strong><font size="5">Genomics Software</font></strong><br /> | <strong><font size="5">Genomics Software</font></strong><br /> | ||
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| − | <table style=" | + | <strong>See also: [http://biosoftware.org Biosoftware.org]<br /> |
| + | </strong><br /> | ||
| + | <table style="BACKGROUND-COLOR: rgb(255,255,255)" height="1653" cellspacing="0" cellpadding="0" width="100%" summary="" border="1"> | ||
<tbody> | <tbody> | ||
<tr> | <tr> | ||
| − | <td><a href="http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html">Alscript</a></td> | + | <td><a href="http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html">Alscript</a> <font color="#999999">by Barton Group</font></td> |
| − | <td>Program to format multiple sequence alignments</td> | + | <td>Program to format multiple sequence alignments by Geof Barton group.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><a href="http:// | + | <td><a href="http://engels.genetics.wisc.edu/amplify/">Amplify</a></td> |
| − | <td>Macintosh program for simulating and testing PCRs | + | <td>Amplify is a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs). </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.ebi.ac.uk/biocat/index.html">Biocatalogue</a></td> | <td><a href="http://www.ebi.ac.uk/biocat/index.html">Biocatalogue</a></td> | ||
| − | <td> | + | <td>EBI software directory of general interest in molecular biology and genetics.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td><a href="http://www.bioexplorer.net/toolbar/">Bioexplorer Toolbar</a></td> | <td><a href="http://www.bioexplorer.net/toolbar/">Bioexplorer Toolbar</a></td> | ||
| − | <td> | + | <td> An easy toolbar for NCBI databases</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>[[BioPAX]]</td> | <td>[[BioPAX]]</td> | ||
| − | <td>Develop a common exchange format for biological pathways data.</td> | + | <td> Develop a common exchange format for biological pathways data.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><a href="http://www. | + | <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm">Biotech Resource</a><font color="#c0c0c0"> at UNM.edu</font></td> |
| − | <td> | + | <td> <font color="#000000" size="2">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><a href=" | + | <td><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/">BLAST at NCBI</a></td> |
| − | <td> | + | <td>Blast open source software</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><a href=" | + | <td> [http://www.ch.embnet.org/software/BOX_form.html BoxShade]</td> |
| − | + | <td> Pretty Printing and Shading of Multiple-Alignment files from <a href="http://www.ch.embnet.org">www.ch.embnet.org</a></td> | |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 71: | Line 69: | ||
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<td><a href="http://genamics.com/software/">Genamics</a></td> | <td><a href="http://genamics.com/software/">Genamics</a></td> | ||
| − | <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><font color="#000000"><a href="http://www.psc.edu/biomed/genedoc/ | + | <td><font color="#000000"><a target="new" href="http://www.psc.edu/biomed/genedoc/">GeneDoc</a></font></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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</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><font color="#000000"><a href="http://www.gsf.de/biodv/matinspector.html | + | <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> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><font color="#000000"><a href="http://compbio.ornl.gov/structure/prospect/ | + | <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> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td><font color="#000000"><a href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html | + | <td><font color="#000000"><a target="new" href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">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> | ||
Latest revision as of 14:39, 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 open source software |
| BoxShade | Pretty Printing and Shading of Multiple-Alignment files from www.ch.embnet.org |
| 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 |
| 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 tools |
| HMMER | HMMER 2.2 Profile hidden Markov models for biological sequence analysis |
| 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 |
