PB Split polytomies - mendessoares/BuddySuite GitHub Wiki

--split_polytomies, -sp

Description

Breaks up all polytomies so each node is bifurcated. The shape of the new subtree created from a polytomy is randomly determined and the distance between the new nodes is kept very small.

Examples

input file: polytomy.newick

(A:1.0,(B:1.0,C:1.0,D:1.0):1.0):1.0;

input tree

#### tree_1 ####
/---------------------------------------------------------------------------- A
|                                                                              
+                                     /-------------------------------------- B
|                                     |                                        
\-------------------------------------+-------------------------------------- C
                                      |                                        
                                      \-------------------------------------- D

usage example 1

$: pb fir.nex -sp

output

(A:1.0,(D:1.0,(C:1.0,B:1.0):1e-06):1.0):1.0;

output tree

#### tree_1 ####
/---------------------------------------------------------------------------- A
+
|                        /--------------------------------------------------- D
\------------------------+
                         |                         /------------------------- C
                         \-------------------------+
                                                   \------------------------- B