Difference between revisions of "Search for Softwares"

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<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>
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<strong><font size="5">Genomics Software</font></strong><br />
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<br />
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<strong>See also: [http://biosoftware.org Biosoftware.org]<br />
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</strong><br />
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<table style="BACKGROUND-COLOR: rgb(255,255,255)" height="1653" cellspacing="0" cellpadding="0" width="100%" summary="" border="1">
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    <tbody>
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        <tr>
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            <td><a href="http://www.compbio.dundee.ac.uk/Software/Alscript/alscript.html">Alscript</a>&nbsp;<font color="#999999">by Barton Group</font></td>
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            <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>
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            <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>
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            <td>EBI software directory of general interest in molecular biology and genetics.</td>
 +
        </tr>
 +
        <tr>
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            <td><a href="http://www.bioexplorer.net/toolbar/">Bioexplorer Toolbar</a></td>
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            <td>&nbsp;An easy toolbar for NCBI databases</td>
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        </tr>
 +
        <tr>
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            <td>[[BioPAX]]</td>
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            <td>&nbsp;Develop a common exchange format for biological pathways data.</td>
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        </tr>
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        <tr>
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            <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm">Biotech Resource</a><font color="#c0c0c0">&nbsp;at UNM.edu</font></td>
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            <td>&nbsp;<font color="#000000" size="2">Free Software that is Relevant to the Molecular Biology and Structural Biology Fields</font></td>
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        </tr>
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        <tr>
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            <td><a href="ftp://ftp.ncbi.nlm.nih.gov/blast/">BLAST at NCBI</a></td>
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            <td>Blast open source software</td>
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        </tr>
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        <tr>
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            <td>&nbsp;[http://www.ch.embnet.org/software/BOX_form.html BoxShade]</td>
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            <td>&nbsp;Pretty Printing and Shading of Multiple-Alignment files from <a href="http://www.ch.embnet.org">www.ch.embnet.org</a></td>
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        </tr>
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        <tr>
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            <td><a href="http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml">Cn3D</a></td>
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            <td>Application that allows to view 3D structures, at NCBI</td>
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        </tr>
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        <tr>
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            <td valign="top"><a href="http://www.clcbio.com/index.php?area=software&amp;section=free">CLC Bio</a><br />
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            </td>
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            <td valign="top">Basic bioinformatics analyses and data management - free download<br />
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            </td>
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        </tr>
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        <tr>
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            <td><font color="#000000"><a href="http://compbio.ornl.gov/structure/domainparser/">DomainParser</a></font></td>
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            <td><font color="#000000">A protein domain partition program</font></td>
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        </tr>
 +
        <tr>
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            <td><a href="http://www.emboss.org/">EMBOSS</a></td>
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            <td>EMBOSS is a package of FREE open source software for sequence analysis</td>
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        </tr>
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        <tr>
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            <td><a href="http://www.e-cell.org/">E-cell</a></td>
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            <td>Simulating intracellular molecular processes of living cells project</td>
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        </tr>
 +
        <tr>
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            <td><a href="http://www.extropia.com/applications.html">eXtropia</a></td>
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            <td>Several free web tools</td>
 +
        </tr>
 +
        <tr>
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            <td><a href="ftp://ftp.virginia.edu/pub/fasta/">Fasta</a></td>
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            <td>Open source for Fasta</td>
 +
        </tr>
 +
        <tr>
 +
            <td><a href="http://genamics.com/software/">Genamics</a></td>
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            <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><font color="#000000"><a target="new" href="http://www.psc.edu/biomed/genedoc/">GeneDoc</a></font></td>
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            <td><font color="#000000">Multiple sequence alignment editor, analyzer &amp; 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>
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            <td>Information about GEneral NEural SImulation System</td>
 +
        </tr>
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        <tr>
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            <td><a href="http://globin.cse.psu.edu/">Globin</a></td>
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            <td>Several free tools</td>
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        </tr>
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        <tr>
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            <td><a href="http://www.gnu.org/">GNU</a></td>
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            <td>Free software foundation - several tools</td>
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        </tr>
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        <tr>
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            <td><a href="http://hmmer.wustl.edu/">HMMER</a></td>
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            <td>HMMER 2.2 Profile hidden Markov models for biological sequence analysis&nbsp;</td>
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        </tr>
 +
        <tr>
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            <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&trade; RT Software (Sequenom)</font></a>&nbsp;</td>
 +
            <td>&nbsp;</td>
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        </tr>
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        <tr>
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            <td><font color="#000000"><a target="new" href="http://www.gsf.de/biodv/matinspector.html">MatInspector</a></font></td>
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            <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>
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            <td><a href="http://www.mbshortcuts.com/software/index.htm">MB Shotcuts</a></td>
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            <td>List of several free molecular biology softwares</td>
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        </tr>
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        <tr>
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            <td><a href="http://www.arc.unm.edu/~aroberts/main/free.htm">MolBio Links</a></td>
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            <td>Links to several molecular biology toos</td>
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        </tr>
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        <tr>
 +
            <td><font color="#000000"><a href="http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/Listings.html">Molecular Biology</a></font></td>
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            <td>List of many free software package for Mac and PC</td>
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        </tr>
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        <tr>
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            <td><font color="#000000"><a href="http://theory.lcs.mit.edu/~elwolf/multicoil.html">Multicoil</a></font></td>
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            <td><font color="#000000">Program to p</font>redict coiled coil regions in proteins</td>
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        </tr>
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        <tr>
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            <td style="VERTICAL-ALIGN: top"><a href="http://www.drive5.com/muscle/">MUSCLE</a><br />
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            </td>
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            <td style="VERTICAL-ALIGN: top">Protein Multiple Sequence Alignment Software<br />
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            </td>
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        </tr>
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        <tr>
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            <td valign="top"><a href="http://www.softgenetics.com/">MutationSurveyor</a><a href="http://www.softgenetics.com/"> &amp; MutationExplorer</a></td>
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            <td valign="top">Analysis of DNA variants, SNPs and mutations<br />
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            </td>
 +
        </tr>
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        <tr>
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            <td><a href="http://www.openinformatics.org/">Open Informatics</a></td>
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            <td>Open source softwares</td>
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        </tr>
 +
        <tr>
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            <td><a href="http://www.phrap.org/">Phred, Phrap &amp; Consed</a></td>
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            <td>Sequence quality and assembly softwares</td>
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        </tr>
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        <tr>
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            <td style="VERTICAL-ALIGN: top"><a href="http://chum.gs.washington.edu/PolyPhred.html">PolyPhred</a><br />
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            </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>
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            <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>
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        </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>

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
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