Commands/prunmajor

From TNT

PRUNMAJOR
Version: 1.1.
Menu path: to do.

PRUNMAJOR
   Use a quick-and-dirty heuristic to identify taxa to prune 
   in order to improve majority rule or frequency difference 
   trees.  It checks by reference to specific groups (i.e. groups 
   present in a reference tree).  General syntax is (defaults in 
   square brackets): 
               prunmaj T N1 N2 N3 .. Nn / S / L ;  
   where T is number of reference tree [mandatory], N1-Nn are node numbers 
   [all], S is the set of trees to consider [all], and L is the list of  
   taxa to exclude [none].  Additional arguments that can precede number  
   of reference tree: 
      &P      group proportion [0.333].  Set only, don't run. 
      [X Y    cost of removal inside (X) and outside (Y) [1,1]. Set only, 
              don't run. 
      +       show pruns for each node of tree T [don't]. 
      =N      show the best N values [1]. 
      *       try to improve frequency differences, rather than 
              just frequencies. 
   It is possible to add/remove taxa from taxon-groups, as final 
   arguments:  
       >G      add taxa with best N values to group G. 
       <G      ditto, removing. 
   The values are presented with an arbitrary rescaling between 0 and 
   1, with taxa having higher scores expected (recall this is a heuristic!)  
   to improve results the most.

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Example: Once you have our cladograms, you want know which taxa could be excluded in the majority rule or frequency difference trees. Imagine you have 5 equally parsimonious trees and you are working on the number 3. The interesting taxon is in the node 21 and you want to see the pruns.

 You are looking for taxa to prune within the nodes 14 and 17-21, working on the tree
 number 3 and you will see the pruning on the resulting tree.