
                             EMBOSS: ednainvar
     _________________________________________________________________
   
                               Program ednainvar
                                       
Function

   Conversion of PHYLIP's dnainvar
   
Description

   EDNAINVAR -- Embossified program to compute Lake's and Cavender's
   phylogenetic invariants from nucleotide sequences
   
   Phylip dnainvar documentation.
   
Usage

   Here is a sample session with ednainvar using the data :-
   4   13
Alpha     AACGTGGCCAAAT
Beta      AAGGTCGCCAAAC
Gamma     CATTTCGTCACAA
Delta     GGTATTTCGGCCT


% ednainvar test

Nucleic acid sequence Invariants method
Output file [ednainvar.outfile]: stdout

Nucleic acid sequence Invariants method, version 3.573c



   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
   III    0    -     0   =     0       1.0000               no


Cavender's quadratic invariants (type L) using purines vs. pyrimidines
 (these are expected to be zero, and thus have a nonsignificant
  chi-square, 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.

  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



Command line arguments

   Mandatory qualifiers:
  [-msf]               seqset     File containing sequences
  [-outfile]           outfile    Output file name

   Optional qualifiers:
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run

   Advanced qualifiers: (none)
   
   Mandatory qualifiers Allowed values Default
   [-msf]
   (Parameter 1) File containing sequences Readable sequences Required
   [-outfile]
   (Parameter 2) Output file name Output file ednainvar.outfile
   Optional qualifiers Allowed values Default
   -printdata Print out the data at start of run Yes/No No
   -progress Print indications of progress of run Yes/No No
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

   (c) Copyright 1986-1993 by Joseph Felsenstein and by the University of
   Washington. Written by Joseph Felsenstein. Permission is granted to
   copy this document provided that no fee is charged for it and that
   this copyright notice is not removed.
   
   This application was modified for inclusion in EMBOSS by Ian Longden
   (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome
   Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
   
Priority

Target users

Comments
