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Last update on 04. Dec 2013 .
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Mark long branches

OCCURRENCE

ARB_NT

 

DESCRIPTION

Badly aligned sequences often result in long branches in the tree. Being able to identify those branches quickly helps to find those sequences.

The programs allows to mark all species having an extra long branch compared with it's neighbour branch.

Enter two values separated by comma into the input field:
   * first the minimum relative difference between two neighbour
     branches you want to have marked.
  • Examples:

    100 = mark branches that have more than the double length
          compared with their neighbour branch
    10  = mark branches that are more than 10% longer 
    0   = mark branches that are longer than their neighbour branch

  • * second the minimun absolute difference between two neighbour
      branches. The unit is the same as used in branchlength.

 

NOTES

If a branch was marked - it's parent branches will not be marked, i.e. the function does not mark ALL extra long branches, only those nearest to the tips of the trees will get marked - otherwise the output won't be useful.

Intended workflow is:
         * Search long branches
         * Check alignment and data and maybe fix it
         * Recalculate tree parts (see ´Add Marked Species and Local Optimization´)
         * Search again. Now you most likely will find other branches.
      

 

EXAMPLES

None

 

WARNINGS

None

 

BUGS

No bugs known