Restriction site maximum likelihood method
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-datafile]          infile     Phylip restml program input file
*  -datasets           integer    [2] Number of sets (Integer 2 or more)
*  -random             toggle     [N] Randomize input order of species
*  -randseed           integer    [3] Random number seed (must be odd) (Any
                                  integer value)
*  -randtimes          integer    [3] How many times to randomise (Any integer
                                  value)
*  -outgnum            integer    [1] Number of the outgroup (Integer 1 or
                                  more)
  [-outfile]           outfile    [erestml.outfile] Phylip restml program
                                  output file
  [-[no]trout]         toggle     [Y] Create a tree file
*  -treefile           outfile    [erestml.treefile] Phylip tree output file

   Additional (Optional) qualifiers (* if not always prompted):
   -multsets           toggle     [N] Analyze multiple data sets
   -[no]besttree       toggle     [Y] Search for best tree
   -og                 toggle     [N] Outgroup root
   -[no]allsites       boolean    [Y] Are all sites detected
*  -lengths            boolean    [N] Use lengths from user trees
   -sitelen            integer    [6] Site length (Integer from 1 to 8)
   -extrap             float      [100.0] Extrapolation factor (Number 0.001
                                  or more)
*  -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

   5   13   2
Alpha     ++-+-++--+++-
Beta      ++++--+--+++-
Gamma     -+--+-++-+-++
Delta     ++-+----++---
Epsilon   ++++----++---

Restriction site Maximum Likelihood method, version 3.57c.650


  Recognition sequences all 6 bases long

Sites absent from all species are assumed to have been omitted




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


remember: this is an unrooted tree!

Ln Likelihood =   -40.35857

Examined   15 trees
 
 Between        And            Length      Approx. Confidence Limits
 -------        ---            ------      ------- ---------- ------
   2             3            0.05855     (  0.05681,     0.06030) **
   3          Epsilon         0.00005     (  0.00000,     0.00010)
   3          Delta           0.01458     (  0.01374,     0.01543) **
   2             1            0.00002     (     zero,     0.00006)
   1          Gamma           0.11430     (  0.11177,     0.11683) **
   1          Beta            0.00008     (  0.00002,     0.00014)
   2          Alpha           0.02468     (  0.02357,     0.02578) **

     *  = significantly positive, P < 0.05
     ** = significantly positive, P < 0.01

((Epsilon:0.00005,Delta:0.01458):0.05855,(Gamma:0.11430,
Beta:0.00008):0.00002,Alpha:0.02468);