Mixed parsimony algorithm
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-infile]            infile     Phylip mix program input file
*  -datasets           integer    [0] How many data sets (Any integer value)
   -method             menu       [Wag] Choose the method to use (Values: Wag
                                  (Wagner); Cam (Camin-Sokal); Mix (Mixed))
*  -randseed           integer    [0] Random number seed (must be odd) (Any
                                  integer value)
*  -randtimes          integer    [0] Number of times to jumble (Any integer
                                  value)
   -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    [emix.outfile] Phylip mix program output
                                  file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [emix.treefile] Phylip tree output file

   Additional (Optional) qualifiers (* if not always prompted):
   -ancestral          boolean    [N] Use ancestral states in input file
   -multsets           toggle     [N] Analyze multiple data sets
   -[no]besttree       toggle     [Y] Search for best tree
*  -random             toggle     [N] Randomize input order of species
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -statesatnodes      boolean    [N] Print states at all nodes of tree
   -steps              boolean    [N] Print out steps in each character
   -[no]drawtree       boolean    [Y] Draw tree

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

   Associated qualifiers:

   "-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

     5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Wagner parsimony method


               


     4 trees in all found




           +--Epsilon   
     +-----4  
     !     +--Gamma     
  +--2  
  !  !     +--Delta     
--1  +-----3  
  !        +--Beta      
  !  
  +-----------Alpha     

  remember: this is an unrooted tree!


requires a total of      9.000





     +--------Gamma     
     !  
  +--2     +--Epsilon   
  !  !  +--4  
  !  +--3  +--Delta     
--1     !  
  !     +-----Beta      
  !  
  +-----------Alpha     

  remember: this is an unrooted tree!


requires a total of      9.000





     +--------Epsilon   
  +--4  
  !  !  +-----Gamma     
  !  +--2  
--1     !  +--Delta     
  !     +--3  
  !        +--Beta      
  !  
  +-----------Alpha     

  remember: this is an unrooted tree!


requires a total of      9.000





     +--------Gamma     
  +--2  
  !  !  +-----Epsilon   
  !  +--4  
--1     !  +--Delta     
  !     +--3  
  !        +--Beta      
  !  
  +-----------Alpha     

  remember: this is an unrooted tree!


requires a total of      9.000

(((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.2500];
((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.2500];
((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.2500];
((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.2500];