Packages

From Bio-nix

Please feel free to add the list of Packages that you want to support and the corresponding URL


Contents

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Emboss 

  Official Home     http://emboss.sourceforge.net/
  Source            ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-3.0.0.tar.gz
  License           GPL and Library GPL


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BioPerl 


  Official Home     http://bioperl.org/wiki/Main_Page
  Core Modules      http://bioperl.org/DIST/current_core_stable.tar.bz2
  Run Modules       http://bioperl.org/DIST/current_run_stable.tar.bz2
  C Extn Modules    http://bioperl.org/DIST/current_ext_stable.tar.bz2
  License           Perl Artistic License


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BioRuby 


   Official Home    http://www.bioruby.org/
   Source           http://bioruby.org/archive/bioruby-1.0.0.tar.gz
   License          GPL <verify>


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BioJava 


   Official Home    http://biojava.open-bio.org/wiki/Main_Page
   Source           http://www.biojava.org/download/source/biojava-1.4.tar.gz
   License          Lesser GPL


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BioPython 


   Official Home    http://www.biopython.org/
   Source           http://www.biopython.org/files/biopython-1.41.tar.gz
   License          Biopython License



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BLAST 

   Official Home    http://www.ncbi.nlm.nih.gov/blast/index.shtml
   Source           ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/blast-2.2.13-ia32-linux.tar.gz 
   License          Public Domain (GPL <Please find out>)


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ClustalX 


   Official Home     http://bips.u-strasbg.fr/fr/Documentation/ClustalX/
   FTP Site          ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/
   License           <Please find out>


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Glimmer 


   Official Home     http://glimmer.sourceforge.net/
   Source            http://prdownloads.sourceforge.net/glimmer/glimmer-1.2.1.tar.gz
   License           GPL


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GROMACS 


   Official Home     http://www.gromacs.org/
   Source            ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.tar.gz
   License           GPL


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HMMER 

   Official Home     http://hmmer.wustl.edu/
   Source            ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.2/hmmer-2.3.2.tar.gz
   License           GPL


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Scilab 

   Official Home     http://www.scilab.org/
   Source            http://www.scilab.org/download/stable/scilab-4.0-src.tar.gz
   Help Manual       http://www.scilab.org/download/stable/man-eng-scilab-4.0.tar.gz
   License           http://www.scilab.org/legal/license.html


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SPDBV 


  Official Home     http://www.expasy.org/spdbv/
  Source            http://www.expasy.org/spdbv/program/spdbv37sp5-Linux.tar.gz
  License           GPL <Please find out>


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RasMol 


  Official Home     http://www.openrasmol.org/
  Source            http://www.bernstein-plus-sons.com/software/RasMol_2.7.2.1.1.tar.gz
  License           GPL


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Octave 


  Official Home    http://www.octave.org/
  Source           ftp://ftp.octave.org/pub/octave/obsolete/octave-2.0.17.tar.gz
  Help Manual      http://www.octave.org/help.html
  License          http://www.octave.org/license.html


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Gnuplot 


  Official Home    http://www.gnuplot.info/
  Source           ftp://ftp.gnuplot.info/pub/gnuplot/gnuplot-4.0.0.tar.gz
  License      http://cvs.sourceforge.net/viewcvs.py/gnuplot/gnuplot/Copyright?view=auto


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Pajek 


  Official Home    http://vlado.fmf.uni-lj.si/pub/networks/pajek/
  Source           http://vlado.fmf.uni-lj.si/pub/networks/pajek/pajek113.exe
  Manual           http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/pajekman.pdf
  Tutotial_for_linux  http://guinness.ffn.ub.es/pajek_tutorial/pajek.html


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Primer3 


  Official Home   http://frodo.wi.mit.edu/primer3/primer3_code.html
  Source          http://frodo.wi.mit.edu/primer3/primer3_1.0.0.tar.gz
  License and Tutotial http://frodo.wi.mit.edu/primer3/README.primer3_1.0.0
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