Continuous character maximum likelihood method
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-infile]            infile     Phylip contml program input file
*  -all                boolean    [N] Input file has all alleles at each locus
   -[no]besttree       toggle     [Y] Search for best tree
*  -lengths            boolean    [N] Use lengths from user trees
*  -global             boolean    [N] Global rearrangements
*  -random             toggle     [N] Randomize input order of species
*  -randseed           integer    [3] Random number seed (must be odd) (Any
                                  integer value)
   -og                 toggle     [N] Outgroup root
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
   -multsets           toggle     [N] Analyze multiple data sets
*  -datasets           integer    [1] How many data sets (Integer 1 or more)
  [-outfile]           outfile    [econtml.outfile] Phylip contml program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [econtml.treefile] Phylip tree output file

   Additional (Optional) qualifiers:
   -continuous         toggle     [N] Continuous characters (else Gene
                                  frequencies)
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run
   -[no]drawtree       boolean    [Y] Draw tree

   Advanced (Unprompted) qualifiers: (none)
   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    10
2 2 2 2 2 2 2 2 2 2
European   0.2868 0.5684 0.4422 0.4286 0.3828 0.7285 0.6386 0.0205
0.8055 0.5043
African    0.1356 0.4840 0.0602 0.0397 0.5977 0.9675 0.9511 0.0600
0.7582 0.6207
Chinese    0.1628 0.5958 0.7298 1.0000 0.3811 0.7986 0.7782 0.0726
0.7482 0.7334
American   0.0144 0.6990 0.3280 0.7421 0.6606 0.8603 0.7924 0.0000
0.8086 0.8636
Australian 0.1211 0.2274 0.5821 1.0000 0.2018 0.9000 0.9837 0.0396
0.9097 0.2976

   5 Populations,   10 Loci

  +----------------------------------African   
  !  
  !              +--------American  
--1--------------2  
  !              !                    +-----------------------Australian
  !              +--------------------3  
  !                                   +Chinese   
  !  
  +--European  


remember: this is an unrooted tree!

Ln Likelihood =    33.29060

examined   15 trees

Between     And             Length      Approx. Confidence Limits
-------     ---             ------      ------- ---------- ------
  1       African           0.08464   (     0.02351,     0.17917)
  1          2              0.03569   (    -0.00262,     0.09493)
  2       American          0.02094   (    -0.00904,     0.06731)
  2          3              0.05098   (     0.00555,     0.12124)
  3       Australian        0.05959   (     0.01775,     0.12430)
  3       Chinese           0.00221   (    -0.02034,     0.03710)
  1       European          0.00624   (    -0.01948,     0.04601)

(African:0.08464,(American:0.02094,(Australian:0.05959,Chinese:0.00221):0.05098):0.03569,
European:0.00624);