EMBOSS: ednainvar

| ## 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