Opened 7 months ago

#821 new task

embed clustal omega

Reported by: westram Owned by: devel
Priority: major Milestone: wishlist
Component: GDE Version: SVN
Keywords: Cc:

Description

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 tree 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 tree
      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

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