Genomics software - Revision history

Mfursov: UGENE link fixed

2009-02-13T12:00:00Z

UGENE link fixed

Mfursov: a link to UGENE software tool was added

2009-02-13T11:58:44Z

a link to UGENE software tool was added

WikiSysop at 05:29, 17 January 2008

2008-01-17T05:29:46Z

WikiSysop at 07:29, 15 January 2008

2008-01-15T07:29:43Z

WikiSysop at 07:27, 15 January 2008

2008-01-15T07:27:24Z

Show changes

WikiSysop at 05:42, 15 January 2008

2008-01-15T05:42:33Z

New page

Genomics Software 
 
See also: [http://biosoftware.org Biosoftware.org] 
 
<table style="BACKGROUND-COLOR: rgb(255,255,255)" height="1653" cellspacing="0" cellpadding="0" width="100%" summary="" border="1">
<tbody>
<tr>
<td><a href="http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html">Alscript</a> by Barton Group</td>
<td>Program to format multiple sequence alignments by Geof Barton group.</td>
</tr>
<tr>
<td><a href="http://engels.genetics.wisc.edu/amplify/">Amplify</a></td>
<td>Amplify is a freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs). </td>
</tr>
<tr>
<td><a href="http://www.ebi.ac.uk/biocat/index.html">Biocatalogue</a></td>
<td>EBI software directory of general interest in molecular biology and genetics.</td>
</tr>
<tr>
<td><a href="http://www.bioexplorer.net/toolbar/">Bioexplorer Toolbar</a></td>
<td> An easy toolbar for NCBI databases</td>
</tr>
<tr>
<td>[[BioPAX]]</td>
<td> Develop a common exchange format for biological pathways data.</td>
</tr>
<tr>
<td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm">Biotech Resource</a> at UNM.edu</td>
<td> Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</td>
</tr>
<tr>
<td><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/">BLAST at NCBI</a></td>
<td>Blast open source software</td>
</tr>
<tr>
<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>
<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>
</tr>
<tr>
<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>
</tr>
<tr>
<td><a href="http://compbio.ornl.gov/structure/domainparser/">DomainParser</a></td>
<td>A protein domain partition program</td>
</tr>
<tr>
<td><a href="http://www.emboss.org/">EMBOSS</a></td>
<td>EMBOSS is a package of FREE open source software for sequence analysis</td>
</tr>
<tr>
<td><a href="http://www.e-cell.org/">E-cell</a></td>
<td>Simulating intracellular molecular processes of living cells project</td>
</tr>
<tr>
<td><a href="http://www.extropia.com/applications.html">eXtropia</a></td>
<td>Several free web tools</td>
</tr>
<tr>
<td><a href="ftp://ftp.virginia.edu/pub/fasta/">Fasta</a></td>
<td>Open source for Fasta</td>
</tr>
<tr>
<td><a href="http://genamics.com/software/">Genamics</a></td>
<td>Genamics SoftwareSeek is a respository and database of freely-distributable and commercial tools for use in molecular biology and biochemistry</td>
</tr>
<tr>
<td><a target="new" href="http://www.psc.edu/biomed/genedoc/">GeneDoc</a></td>
<td>Multiple sequence alignment editor, analyzer & shading utility for windows</td>
</tr>
<tr>
<td><a href="http://genesis.bbb.caltech.edu/GENESIS/genesis.html">Genesis</a></td>
<td>Information about GEneral NEural SImulation System</td>
</tr>
<tr>
<td><a href="http://globin.cse.psu.edu/">Globin</a></td>
<td>Several free tools</td>
</tr>
<tr>
<td><a href="http://www.gnu.org/">GNU</a></td>
<td>Free software foundation - several tools</td>
</tr>
<tr>
<td><a href="http://hmmer.wustl.edu/">HMMER</a></td>
<td>HMMER 2.2 Profile hidden Markov models for biological sequence analysis </td>
</tr>
<tr>
<td><a href="http://rsb.info.nih.gov/nih-image/">NIH Image</a></td>
<td>Image analysis program for Macintosh from NIH</td>
</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." href="http://www.sequenom.com/genetic_systems/software/software_rt.php">MassARRAY™ RT Software (Sequenom)</a> </td>
<td> </td>
</tr>
<tr>
<td><a target="new" href="http://www.gsf.de/biodv/matinspector.html">MatInspector</a></td>
<td>Detection of transcription factor binding sites</td>
</tr>
<tr>
<td><a href="http://www.scriptarchive.com/">Matt's Script Archive</a></td>
<td>Several free Perl scripts</td>
</tr>
<tr>
<td><a href="http://www.mbshortcuts.com/software/index.htm">MB Shotcuts</a></td>
<td>List of several free molecular biology softwares</td>
</tr>
<tr>
<td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm">MolBio Links</a></td>
<td>Links to several molecular biology toos</td>
</tr>
<tr>
<td><a href="http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/Listings.html">Molecular Biology</a></td>
<td>List of many free software package for Mac and PC</td>
</tr>
<tr>
<td><a href="http://theory.lcs.mit.edu/~elwolf/multicoil.html">Multicoil</a></td>
<td>Program to predict coiled coil regions in proteins</td>
</tr>
<tr>
<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>
</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">Analysis of DNA variants, SNPs and mutations 
</td>
</tr>
<tr>
<td><a href="http://www.openinformatics.org/">Open Informatics</a></td>
<td>Open source softwares</td>
</tr>
<tr>
<td><a href="http://www.phrap.org/">Phred, Phrap & Consed</a></td>
<td>Sequence quality and assembly softwares</td>
</tr>
<tr>
<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>
</tr>
<tr>
<td valign="top"><a href="http://physionet.org/">PhysioNet</a> 
</td>
<td valign="top">Collection of physiologic simulation software 
</td>
</tr>
<tr>
<td><a href="http://www.chemicalgraphics.com/">PovChem</a></td>
<td>Visualization program for PDB protein structures</td>
</tr>
<tr>
<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>
</tr>
<tr>
<td><a target="new" href="http://compbio.ornl.gov/structure/prospect/">Prospect</a></td>
<td>A threading-based protein structure prediction system</td>
</tr>
<tr>
<td><a href="http://lib.stat.cmu.edu/R/CRAN/">R - statistical package</a></td>
<td>Statistical computing and graphics software</td>
</tr>
<tr>
<td><a target="new" href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">TreeView</a></td>
<td>Tree drawing software for Apple Macintosh and Windows</td>
</tr>
<tr>
<td><a href="http://sourceforge.net/softwaremap/trove_list.php?form_cat=252">SourceForge.net</a></td>
<td>Several ready to use tool</td>
</tr>
<tr>
<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>
</tr>
<tr>
<td><a href="http://www.ualberta.ca/~stothard/javascript/d_load.html">Sequence Manipulation</a></td>
<td>Free suite of sequence manipulation tools</td>
</tr>
<tr>
<td><a href="http://blast.wustl.edu/">WU-BLAST</a></td>
<td>Washington university BLAST archives</td>
</tr>
</tbody>
</table>

@@ Line 3: / Line 3: @@
 </font>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">
+<table height="1653" width="100%" cellspacing="0" cellpadding="0" border="1" summary="" style="background-color: rgb(255, 255, 255);">
      <tbody>
          <tr>
@@ Line 31: / Line 31: @@
          <tr>
              <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm"><font color="#810081">Biotech Resource</font></a><font color="#c0c0c0">&nbsp;at UNM.edu</font></td>
-             <td>&nbsp;<font color="#000000" size="2">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></td>
+             <td>&nbsp;<font size="2" color="#000000">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></td>
          </tr>
          <tr>
@@ Line 90: / Line 90: @@
          </tr>
          <tr>
-             <td><a target="new" href="http://www.psc.edu/biomed/genedoc/"><font color="#810081">GeneDoc</font></a></td>
+             <td><a href="http://www.psc.edu/biomed/genedoc/" target="new"><font color="#810081">GeneDoc</font></a></td>
              <td><font color="#000000">&nbsp;Multiple sequence alignment editor, analyzer &amp; shading utility for windows</font></td>
          </tr>
@@ Line 114: / Line 114: @@
          </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." href="http://www.sequenom.com/genetic_systems/software/software_rt.php"><font size="-1">MassARRAY&trade; RT Software (Sequenom)</font></a>&nbsp;</td>
+             <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&trade; RT Software (Sequenom)</font></a>&nbsp;</td>
              <td>&nbsp;</td>
          </tr>
          <tr>
-             <td><font color="#000000"><a target="new" href="http://www.gsf.de/biodv/matinspector.html">MatInspector</a></font></td>
+             <td><font color="#000000"><a href="http://www.gsf.de/biodv/matinspector.html" target="new">MatInspector</a></font></td>
              <td><font color="#000000">&nbsp;Detection of transcription factor binding sites</font></td>
          </tr>
@@ Line 142: / Line 142: @@
          </tr>
          <tr>
-             <td style="VERTICAL-ALIGN: top"><a href="http://www.drive5.com/muscle/">MUSCLE</a></td>
+             <td style="vertical-align: top;"><a href="http://www.drive5.com/muscle/">MUSCLE</a></td>
-             <td style="VERTICAL-ALIGN: top">&nbsp;Protein Multiple Sequence Alignment Software</td>
+             <td style="vertical-align: top;">&nbsp;Protein Multiple Sequence Alignment Software</td>
          </tr>
          <tr>
@@ Line 158: / Line 158: @@
          </tr>
          <tr>
-             <td style="VERTICAL-ALIGN: top"><a href="http://chum.gs.washington.edu/PolyPhred.html">PolyPhred</a></td>
+             <td style="vertical-align: top;"><a href="http://chum.gs.washington.edu/PolyPhred.html">PolyPhred</a></td>
-             <td style="VERTICAL-ALIGN: top">&nbsp;Compares traces to identify heterozygous sites for SNPs</td>
+             <td style="vertical-align: top;">&nbsp;Compares traces to identify heterozygous sites for SNPs</td>
          </tr>
          <tr>
@@ Line 174: / Line 174: @@
          </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 href="http://compbio.ornl.gov/structure/prospect/" target="new">Prospect</a></font></td>
              <td><font color="#000000">&nbsp;A threading-based protein structure prediction system</font></td>
          </tr>
@@ Line 182: / Line 182: @@
          </tr>
          <tr>
-             <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"><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>
          </tr>
@@ Line 204: / Line 204: @@
              <td><a href="http://blast.wustl.edu/">WU-BLAST</a>&nbsp;</td>
              <td>&nbsp;Washington University BLAST archives</td>
          </tr>
      </tbody>
 </table>

@@ Line 20: / Line 20: @@
              <td><a href="http://www.bioexplorer.net/toolbar/"><font color="#810081">Bioexplorer Toolbar</font></a></td>
              <td>&nbsp;An easy toolbar for NCBI databases</td>
          </tr>
          <tr>
@@ Line 28: / Line 32: @@
              <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm"><font color="#810081">Biotech Resource</font></a><font color="#c0c0c0">&nbsp;at UNM.edu</font></td>
              <td>&nbsp;<font color="#000000" size="2">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></td>
          </tr>
          <tr>

@@ Line 206: / Line 206: @@
          </tr>
          <tr>
-             <td><a href="javascript:void(0);/*1234520926215*/">Unipro UGENE</a></td>
+             <td>[http://ugene.unipro.ru UGENE]<br />
              <td>Integrated visual environment for popular command line bioinformatics tools like HMMER, MUSCLE, BLAST, repeats and restriction enzymes analysis etc.</td>
          </tr>
      </tbody>
 </table>

@@ Line 196: / Line 196: @@
              <td><a href="http://www.ualberta.ca/~stothard/javascript/d_load.html">Sequence Manipulation</a></td>
              <td>&nbsp;Free suite of sequence manipulation tools</td>
          </tr>
          <tr>