Fitch-Margoliash and least-squares distance methods
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-infile]            infile     Phylip fitch program input file
*  -datasets           integer    [0] How many data sets (Any integer value)
*  -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)
  [-outfile]           outfile    [efitch.outfile] Phylip fitch program output
                                  file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [*.efitch] Phylip tree output file

   Additional (Optional) qualifiers (* if not always prompted):
   -lt                 boolean    [N] Lower-triangular data matrix
   -ut                 boolean    [N] Upper-triangular data matrix
   -replicates         boolean    [N] Subreplicates
   -multsets           toggle     [N] Analyze multiple data sets
   -[no]besttree       toggle     [Y] Search for best tree
*  -random             toggle     [N] Randomize input order of species
*  -length             boolean    [N] Use lengths from user trees
   -power              float      [3.0] Power (Any numeric value)
   -negbranch          boolean    [N] Negative branch lengths allowed
*  -global             boolean    [N] Global rearrangements
   -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

    7
Bovine      0.0000  1.6866  1.7198  1.6606  1.5243  1.6043  1.5905
Mouse       1.6866  0.0000  1.5232  1.4841  1.4465  1.4389  1.4629
Gibbon      1.7198  1.5232  0.0000  0.7115  0.5958  0.6179  0.5583
Orang       1.6606  1.4841  0.7115  0.0000  0.4631  0.5061  0.4710
Gorilla     1.5243  1.4465  0.5958  0.4631  0.0000  0.3484  0.3083
Chimp       1.6043  1.4389  0.6179  0.5061  0.3484  0.0000  0.2692
Human       1.5905  1.4629  0.5583  0.4710  0.3083  0.2692  0.0000

   7 Populations
                  __ __             2
                  \  \   (Obs - Exp)
Sum of squares =  /_ /_  ------------
                                3
                   i  j      Obs

Negative branch lengths not allowed


  +---------------------------------------------Mouse     
  !  
  !                                 +-----Human     
  !                              +--5  
  !                           +--4  +--------Chimp     
  !                           !  !  
  !                        +--3  +---------Gorilla   
  !                        !  !  
--1------------------------2  +-----------------Orang     
  !                        !  
  !                        +--------------------Gibbon    
  !  
  +------------------------------------------------------Bovine    


remember: this is an unrooted tree!

Sum of squares =     0.01417

examined   45 trees

Between        And            Length
-------        ---            ------
   1          Mouse             0.77028
   1             2              0.41923
   2             3              0.05289
   3             4              0.01693
   4             5              0.03705
   5          Human             0.11417
   5          Chimp             0.15503
   4          Gorilla           0.15677
   3          Orang             0.29628
   2          Gibbon            0.35442
   1          Bovine            0.91632

(Mouse:0.77028,((((Human:0.11417,Chimp:0.15503):0.03705,
Gorilla:0.15677):0.01693,Orang:0.29628):0.05289,Gibbon:0.35442):0.41923,Bovine:0.91632);