
Penny algorithm for Dollo or polymorphism parsimony, version 3.7a
 branch-and-bound to find all most parsimonious trees

Dollo parsimony method

 7 species,   6 characters

Name         Characters
----         ----------

Alpha1       11011 0
Alpha2       11011 0
Beta1        11000 0
Beta2        11000 0
Gamma1       10011 0
Delta        00100 1
Epsilon      00111 0



requires a total of              3.000

    3 trees in all found




  +-----------------Delta     
  !  
--2  +--------------Epsilon   
  !  !  
  +--3  +-----------Gamma1    
     !  !  
     +--6  +--------Alpha2    
        !  !  
        +--1     +--Beta2     
           !  +--5  
           +--4  +--Beta1     
              !  
              +-----Alpha1    


 reversions in each character:
         0   1   2   3   4   5   6   7   8   9
     *-----------------------------------------
    0!       0   0   1   1   1   0            

From    To     Any Steps?    State at upper node
                             ( . means same as in the node below it on tree)

root      2         yes    ..1.. .
  2    Delta        yes    ..... 1
  2       3         yes    ...11 .
  3    Epsilon      no     ..... .
  3       6         yes    1.0.. .
  6    Gamma1       no     ..... .
  6       1         yes    .1... .
  1    Alpha2       no     ..... .
  1       4         no     ..... .
  4       5         yes    ...00 .
  5    Beta2        no     ..... .
  5    Beta1        no     ..... .
  4    Alpha1       no     ..... .





  +-----------------Delta     
  !  
--2  +--------------Epsilon   
  !  !  
  +--3  +-----------Gamma1    
     !  !  
     +--6        +--Beta2     
        !  +-----5  
        !  !     +--Beta1     
        +--4  
           !     +--Alpha2    
           +-----1  
                 +--Alpha1    


 reversions in each character:
         0   1   2   3   4   5   6   7   8   9
     *-----------------------------------------
    0!       0   0   1   1   1   0            

From    To     Any Steps?    State at upper node
                             ( . means same as in the node below it on tree)

root      2         yes    ..1.. .
  2    Delta        yes    ..... 1
  2       3         yes    ...11 .
  3    Epsilon      no     ..... .
  3       6         yes    1.0.. .
  6    Gamma1       no     ..... .
  6       4         yes    .1... .
  4       5         yes    ...00 .
  5    Beta2        no     ..... .
  5    Beta1        no     ..... .
  4       1         no     ..... .
  1    Alpha2       no     ..... .
  1    Alpha1       no     ..... .





  +-----------------Delta     
  !  
--2  +--------------Epsilon   
  !  !  
  +--3  +-----------Gamma1    
     !  !  
     !  !        +--Beta2     
     +--6     +--5  
        !  +--4  +--Beta1     
        !  !  !  
        +--1  +-----Alpha2    
           !  
           +--------Alpha1    


 reversions in each character:
         0   1   2   3   4   5   6   7   8   9
     *-----------------------------------------
    0!       0   0   1   1   1   0            

From    To     Any Steps?    State at upper node
                             ( . means same as in the node below it on tree)

root      2         yes    ..1.. .
  2    Delta        yes    ..... 1
  2       3         yes    ...11 .
  3    Epsilon      no     ..... .
  3       6         yes    1.0.. .
  6    Gamma1       no     ..... .
  6       1         yes    .1... .
  1       4         no     ..... .
  4       5         yes    ...00 .
  5    Beta2        no     ..... .
  5    Beta1        no     ..... .
  4    Alpha2       no     ..... .
  1    Alpha1       no     ..... .


