CSC

% fmove 
Interactive mixed method parsimony
Phylip character discrete states file: move.dat
Phylip tree file (optional): 
NEXT? (R # + - S . T U W O F H J K L C ? X Q) (? for Help): Q
Do you want to write out the tree to a file? (Y or N): Y

 5 species,   6 characters

Wagner parsimony method


Computing steps needed for compatibility in characters...


(unrooted)                    8.0 Steps             4 chars compatible
                            
  ,-----------5:Epsilon   
--9  
  !  ,--------4:Delta     
  `--8  
     !  ,-----3:Gamma     
     `--7  
        !  ,--2:Beta      
        `--6  
           `--1:Alpha     


Tree written to file "move.treefile"

Interactive mixed method parsimony
Version: EMBOSS:6.3.0

   Standard (Mandatory) qualifiers:
  [-infile]            discretestates File containing data set
  [-intreefile]        tree       Phylip tree file (optional)

   Additional (Optional) qualifiers:
   -weights            properties Weights file
   -ancfile            properties Ancestral states file
   -factorfile         properties Factors file
   -method             menu       [Wagner] Choose the method to use (Values: w
                                  (Wagner); c (Camin-Sokal); m (Mixed))
   -outgrno            integer    [0] Species number to use as outgroup
                                  (Integer 0 or more)
   -threshold          float      [$(infile.discretesize)] Threshold value
                                  (Number 0.000 or more)
   -initialtree        menu       [Arbitary] Initial tree (Values: a
                                  (Arbitary); u (User); s (Specify))
   -screenwidth        integer    [80] Width of terminal screen in characters
                                  (Any integer value)
   -screenlines        integer    [24] Number of lines on screen (Any integer
                                  value)
   -outtreefile        outfile    [*.fmove] Phylip tree output file (optional)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outtreefile" 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

(Epsilon,(Delta,(Gamma,(Beta,Alpha))));