List of applications executed via Biopython

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(Python libraries: added pygraphviz/pydot; looks like matplotlib is Phylo-specific, too)
(Applications: added Bio.Align.Applications)
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===Applications===
 
===Applications===
  
Bio.Phylo:
+
Bio.Align:
  
* [http://www.microbesonline.org/fasttree/ FastTree]
+
* [http://www.clustal.org/omega/ Clustal Omega]
* [http://www.atgc-montpellier.fr/phyml/ PhyML]
+
* [http://www.clustal.org/clustal2/ Clustal W]
* [http://sco.h-its.org/exelixis/web/software/raxml/index.html RAxML]
+
* [http://bibiserv.techfak.uni-bielefeld.de/dialign/ DIALIGN]
* [http://abacus.gene.ucl.ac.uk/software/ PAML] (baseml, codeml, yn00)
+
* [http://msaprobs.sourceforge.net/homepage.htm MSAProbs]
 +
* [http://mafft.cbrc.jp/alignment/software/ MAFFT]
 +
* [http://www.drive5.com/muscle/ MUSCLE]
 +
* [http://code.google.com/p/prank-msa/ PRANK]
 +
* [http://probcons.stanford.edu/ ProbCons]
 +
* [http://www.tcoffee.org/ T-Coffee]
  
 
Bio.PDB:
 
Bio.PDB:
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* [http://www.e-lucid.com/i/software/bioinformatics/naccess.html NACCESS]
 
* [http://www.e-lucid.com/i/software/bioinformatics/naccess.html NACCESS]
 
* [ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/ PSEA]
 
* [ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/ PSEA]
 +
 +
Bio.Phylo:
 +
 +
* [http://www.microbesonline.org/fasttree/ FastTree]
 +
* [http://www.atgc-montpellier.fr/phyml/ PhyML]
 +
* [http://sco.h-its.org/exelixis/web/software/raxml/index.html RAxML]
 +
* [http://abacus.gene.ucl.ac.uk/software/ PAML] (baseml, codeml, yn00)
  
 
''I am not particularly fond of the title of this page (tiago), if you have a better one, please correct''
 
''I am not particularly fond of the title of this page (tiago), if you have a better one, please correct''

Revision as of 07:33, 10 December 2013

(under construction)

Python libraries

NumPy

Reportlab (Bio.Graphics only)

Matplotlib (Bio.Phylo.draw and draw_graphviz only)

RDFLib (Bio.Phylo.CDAOIO only)

NetworkX (Bio.Phylo.to_networkx and draw_graphviz only)

PyGraphviz or Pydot (Bio.Phylo.draw_graphviz only)

Applications

Bio.Align:

Bio.PDB:

Bio.Phylo:

I am not particularly fond of the title of this page (tiago), if you have a better one, please correct

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