embed clustal omega

[westram]

Available at ​http://www.clustal.org/omega/
Usage at ​http://www.clustal.org/omega/README

Wanted features:

1. support all sequence types (RNA,DNA,AA)
2. profile alignment (optional)
   • align sequences to existing alignment w/o changing the latter
   • possibilities to define profile:
     • in extra step: e.g. Button Create profile from marked
     • select existing species-config (and create profile from members)
3. guidetree alignment (optional)
   • select a to activate
4. allow to choose whether to export aligned or unaligned sequences
   • clustering in clustal-omega is affected by alignment
   • using aligned sequences allows iterative procedure:
     1. align sequences
     2. construct an initial
     3. optimize alignment (using improved guidetree)
     4. optimize guidetree (using improved alignment)
     5. goto c.
5. allow clustal-omega-internal guidetree/profile iterations
   • see options --iter and related