.. -*- coding: utf-8 -*-

=============================
 Multiple Sequence Alignment
=============================

From :ref:`MultiSeq <multiseq>`, export sequences in FASTA format
(:menuselection:`File --> Export`: All Sequences, Sequence Data
(FASTA), Include sources in FASTA header).

Create a multiple sequence alignment(MSA) with MAFFT_ (or ClustaLW or
tCOFFE or Muscle). Here we use the MAFFT server:

Upload to the `MAFFT server`_  (use defaults).

- download alignment (ALN and FASTA) (Save link as
  ``adk_msa_mafft.aln`` (Clustal MSA format) and
  ``adk_msa_mafft.fasta`` (FASTA))
- visualize the phylogenetic tree
- visualize the alignment (see also Jalview_)

Then use your saved alignment to create a `WebLogo`_ (check
:guilabel:`Multiline Logo`). Download as PDF or PNG.
 
.. seealso::
   Many different `alignment servers`_
   
   - MUSCLE_ http://www.ebi.ac.uk/Tools/msa/muscle/
   - MAFFT_ http://mafft.cbrc.jp/alignment/server/ or
     http://www.ebi.ac.uk/Tools/msa/mafft/
   - Tcoffee_  http://tcoffee.crg.cat/apps/tcoffee/do:regular
   - ClustalW_ http://www.ebi.ac.uk/Tools/msa/clustalw2/

.. _MAFFT server: http://mafft.cbrc.jp/alignment/server/
.. _MAFFT: http://mafft.cbrc.jp/alignment/software/
.. _MUSCLE: http://drive5.com/muscle/
.. _Tcoffee: http://www.tcoffee.org/
.. _ClustalW: http://www.clustal.org/
.. _alignment servers: http://www.expasy.org/genomics/sequence_alignment
.. _WebLogo: http://weblogo.berkeley.edu/logo.cgi
.. _Jalview: http://www.jalview.org/