Nucleic acid sequence invariants method
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing sequences
  [-outfile]           outfile    [ednainvar.outfile] Phylip dnainvar program
                                  output file

   Additional (Optional) qualifiers:
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run

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

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        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

   4   13
Alpha     AACGTGGCCAAAT
Beta      AAGGTCGCCAAAC
Gamma     CATTTCGTCACAA
Delta     GGTATTTCGGCCT

Nucleic acid sequence Invariants method, version 3.57c.650


   Pattern   Number of times

     AAAC         1
     AAAG         2
     AACC         1
     AACG         1
     CCCG         1
     CCTC         1
     CGTT         1
     GCCT         1
     GGGT         1
     GGTA         1
     TCAT         1
     TTTT         1


Symmetrized patterns (1, 2 = the two purines  and  3, 4 = the two pyrimidines
                  or  1, 2 = the two pyrimidines  and  3, 4 = the two purines)

     1111         1
     1112         2
     1113         3
     1121         1
     1132         2
     1133         1
     1231         1
     1322         1
     1334         1

Tree topologies (unrooted): 

    I:  ((Alpha,Beta),(Gamma,Delta))
   II:  ((Alpha,Gamma),(Beta,Delta))
  III:  ((Alpha,Delta),(Beta,Gamma))


Lake's linear invariants
 (these are expected to be zero for the two incorrect tree topologies.
  This is tested by testing the equality of the two parts
  of each expression using a one-sided exact binomial test.
  The null hypothesis is that the first part is no larger than the second.)

 Tree                             Exact test P value    Significant?

   I      1    -     0   =     1       0.5000               no
   II     0    -     0   =     0       1.0000               no


  [Part of this file has been deleted for brevity]

different purine:pyrimidine ratios from 1:1.

  Tree I:

   Contingency Table

      2     8
      1     2

   Quadratic invariant =             4.0

   Chi-square =    0.23111 (not significant)


  Tree II:

   Contingency Table

      1     5
      1     6

   Quadratic invariant =            -1.0

   Chi-square =    0.01407 (not significant)


  Tree III:

   Contingency Table

      1     2
      6     4

   Quadratic invariant =             8.0

   Chi-square =    0.66032 (not significant)




Cavender's quadratic invariants (type K) using purines vs. pyrimidines
 (these are expected to be zero for the correct tree topology)
They will be misled if there are substantially
different evolutionary rate between sites, or
different purine:pyrimidine ratios from 1:1.
No statistical test is done on them here.

  Tree I:              -9.0
  Tree II:              4.0
  Tree III:             5.0