Included Tools
==============

.. _msa:

Multiple Sequence Alignment
---------------------------

* `Clustal Omega`_ (version 1.2.4)
* `ClustalW`_ (version 2.1)
* `Mafft`_ (version 7.310)
* `Muscle`_ (version 3.8.31)
* `T-coffee`_ (version 11.00.8cbe486)
* `Probcons`_ (version 1.12)
* `MSAProbs`_ (version 0.9.7)
* `GLProbs`_ (version 0.9.7)


.. _pdis:

Protein Disorder Prediction
---------------------------

* `DisEMBL`_ (version 1.5)
* `IUPred`_ (version 1.0)
* Jronn - Java implementation of `Ronn`_ (version 3.1)
* `GlobPlot`_ (version 2.3)

.. _aac:

Amino Acid Conservation
-----------------------

* `AACon`_ (version 1.0)


.. _rnass:

RNA Secondary Structure
-----------------------

* RNAalifold from `ViennaRNA`_ (version 2.0)


.. _Clustal Omega: http://www.clustal.org/omega
.. _ClustalW: http://www.clustal.org/clustal2
.. _Mafft: http://align.bmr.kyushu-u.ac.jp/mafft/software/
.. _Muscle: http://www.drive5.com/muscle
.. _T-coffee: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
.. _Probcons: http://probcons.stanford.edu/
.. _MSAProbs: http://msaprobs.sourceforge.net/
.. _GLProbs: http://sourceforge.net/projects/glprobs/
.. _DisEMBL: http://dis.embl.de/
.. _IUPred: http://iupred.enzim.hu
.. _Ronn: http://www.strubi.ox.ac.uk/RONN
.. _GlobPlot: http://globplot.embl.de/
.. _AACon: http://www.compbio.dundee.ac.uk/aacon
.. _ViennaRNA: http://www.tbi.univie.ac.at/RNA