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<strong><font size="5">Genomics Software<br />
<br />
</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">
<tbody>
<tr>
<td><a href="http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html"><font color="#810081">Alscript</font></a> <font color="#999999">by Barton Group</font></td>
<td>Program to format multiple sequence alignments by Geof Barton group.</td>
</tr>
<tr>
<td><a href="http://engels.genetics.wisc.edu/amplify/"><font color="#810081">Amplify</font></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"><font color="#810081">Biocatalogue</font></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/"><font color="#810081">Bioexplorer Toolbar</font></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"><font color="#810081">Biotech Resource</font></a><font color="#c0c0c0"> at UNM.edu</font></td>
<td> <font color="#000000" size="2">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></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><br />
</td>
<td valign="top">Basic bioinformatics analyses and data management - free download<br />
</td>
</tr>
<tr>
<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>
</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/"><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>
</tr>
<tr>
<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>
</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"><font size="-1">MassARRAY™ RT Software (Sequenom)</font></a> </td>
<td> </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">Detection of transcription factor binding sites</font></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"><font color="#810081">MolBio Links</font></a></td>
<td>Links to several molecular biology toos</td>
</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>List of many free software package for Mac and PC</td>
</tr>
<tr>
<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>
</tr>
<tr>
<td style="VERTICAL-ALIGN: top"><a href="http://www.drive5.com/muscle/">MUSCLE</a><br />
</td>
<td style="VERTICAL-ALIGN: top">Protein Multiple Sequence Alignment Software<br />
</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<br />
</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><br />
</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><br />
</td>
<td valign="top">Collection of physiologic simulation software<br />
</td>
</tr>
<tr>
<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>
</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><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>
</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><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>
</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>
<br />
</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">
<tbody>
<tr>
<td><a href="http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html"><font color="#810081">Alscript</font></a> <font color="#999999">by Barton Group</font></td>
<td>Program to format multiple sequence alignments by Geof Barton group.</td>
</tr>
<tr>
<td><a href="http://engels.genetics.wisc.edu/amplify/"><font color="#810081">Amplify</font></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"><font color="#810081">Biocatalogue</font></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/"><font color="#810081">Bioexplorer Toolbar</font></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"><font color="#810081">Biotech Resource</font></a><font color="#c0c0c0"> at UNM.edu</font></td>
<td> <font color="#000000" size="2">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></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><br />
</td>
<td valign="top">Basic bioinformatics analyses and data management - free download<br />
</td>
</tr>
<tr>
<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>
</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/"><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>
</tr>
<tr>
<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>
</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"><font size="-1">MassARRAY™ RT Software (Sequenom)</font></a> </td>
<td> </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">Detection of transcription factor binding sites</font></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"><font color="#810081">MolBio Links</font></a></td>
<td>Links to several molecular biology toos</td>
</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>List of many free software package for Mac and PC</td>
</tr>
<tr>
<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>
</tr>
<tr>
<td style="VERTICAL-ALIGN: top"><a href="http://www.drive5.com/muscle/">MUSCLE</a><br />
</td>
<td style="VERTICAL-ALIGN: top">Protein Multiple Sequence Alignment Software<br />
</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<br />
</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><br />
</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><br />
</td>
<td valign="top">Collection of physiologic simulation software<br />
</td>
</tr>
<tr>
<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>
</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><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>
</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><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>
</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>
