Penny algorithm for DNA
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqset     File containing a sequence
   -og                 toggle     [N] Outgroup root
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
*  -valthresh          float      [1.0] Threshold value (Number 1.000 or more)
  [-outfile]           outfile    [ednapenny.outfile] Phylip dnapenny program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [ednapenny.treefile] Phylip tree output file

   Additional (Optional) qualifiers:
   -numgroups          integer    [1000] How many groups of 100 trees (Any
                                  integer value)
   -howoften           integer    [100] How often to report, in trees (Any
                                  integer value)
   -simple             boolean    Branch and bound is simple
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -steps              boolean    [N] Print out steps in each site
   -seqatnodes         boolean    [N] Print sequences at all nodes of tree
   -[no]drawtree       boolean    [Y] Draw tree

   Advanced (Unprompted) qualifiers:
   -thresh             toggle     [N] Use Threshold parsimony

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   "-treefile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

    8    6
Alpha1    AAGAAG
Alpha2    AAGAAG
Beta1     AAGGGG
Beta2     AAGGGG
Gamma1    AGGAAG
Gamma2    AGGAAG
Delta     GGAGGA
Epsilon   GGAAAG

Penny algorithm for DNA, version 3.57c.650
 branch-and-bound to find all most parsimonious trees


requires a total of              8.000

     9 trees in all found




  +--------------------Alpha1    
  !  
  !                 +--Delta     
  !              +--3  
  !           +--7  +--Epsilon   
--1           !  !  
  !     +-----6  +-----Gamma2    
  !     !     !  
  !  +--4     +--------Gamma1    
  !  !  !  
  !  !  !           +--Beta2     
  +--2  +-----------5  
     !              +--Beta1     
     !  
     +-----------------Alpha2    

  remember: this is an unrooted tree!





  +--------------------Alpha1    
  !  
  !                 +--Delta     
  !           +-----3  
  !           !     +--Epsilon   
--1     +-----6  
  !     !     !     +--Gamma2    
  !     !     +-----7  
  !  +--4           +--Gamma1    
  !  !  !  
  !  !  !           +--Beta2     
  +--2  +-----------5  
     !              +--Beta1     
     !  
     +-----------------Alpha2    



  [Part of this file has been deleted for brevity]

     !              +--Beta2     
     +--------------5  
                    +--Beta1     

  remember: this is an unrooted tree!





  +--------------------Alpha1    
  !  
  !                 +--Delta     
  !           +-----3  
  !           !     +--Epsilon   
--1        +--6  
  !        !  !     +--Gamma2    
  !  +-----2  +-----7  
  !  !     !        +--Gamma1    
  !  !     !  
  +--4     +-----------Alpha2    
     !  
     !              +--Beta2     
     +--------------5  
                    +--Beta1     

  remember: this is an unrooted tree!





  +--------------------Alpha1    
  !  
  !                 +--Delta     
  !              +--3  
  !           +--6  +--Epsilon   
--1           !  !  
  !        +--7  +-----Gamma1    
  !        !  !  
  !  +-----2  +--------Gamma2    
  !  !     !  
  +--4     +-----------Alpha2    
     !  
     !              +--Beta2     
     +--------------5  
                    +--Beta1     

  remember: this is an unrooted tree!

(Alpha1,(((((Delta,Epsilon),Gamma2),Gamma1),(Beta2,Beta1)),Alpha2))[0.1111];
(Alpha1,((((Delta,Epsilon),(Gamma2,Gamma1)),(Beta2,Beta1)),Alpha2))[0.1111];
(Alpha1,(((((Delta,Epsilon),Gamma1),Gamma2),(Beta2,Beta1)),Alpha2))[0.1111];
(Alpha1,((((Delta,Epsilon),Gamma2),Gamma1),((Beta2,Beta1),Alpha2)))[0.1111];
(Alpha1,(((Delta,Epsilon),(Gamma2,Gamma1)),((Beta2,Beta1),Alpha2)))[0.1111];
(Alpha1,((((Delta,Epsilon),Gamma1),Gamma2),((Beta2,Beta1),Alpha2)))[0.1111];
(Alpha1,(((((Delta,Epsilon),Gamma2),Gamma1),Alpha2),(Beta2,Beta1)))[0.1111];
(Alpha1,((((Delta,Epsilon),(Gamma2,Gamma1)),Alpha2),(Beta2,Beta1)))[0.1111];
(Alpha1,(((((Delta,Epsilon),Gamma1),Gamma2),Alpha2),(Beta2,Beta1)))[0.1111];