## EMBOSS: ednadist

# Program ednadist

## Function

Conversion of PHYLIP's dnadist

## Description

EDNADIST -- Embossified program to compute distance matrix from nucleotide sequences

Phylip dnadist documentation.

## Usage

Here is a sample session with ednadist.

    with the test data of:-

       5   13
    Alpha     AACGTGGCCACAT
    Beta      AAGGTCGCCACAC
    Gamma     CAGTTCGCCACAA
    Delta     GAGATTTCCGCCT
    Epsilon   GAGATCTCCGCCC

    % ednadist test

    Nucleic acid sequence Distance Matrix program
    Output file [ednadist.outfile]: stdout
    Distance methods
        Kimura : Kimura 2-parameter distance
        JinNei : Jin and Nei distance
            ML : Maximum Likelihood distance
         Jukes : Jukes-Cantor distance
    Choose the method to use [Kimura]:
    Transition/transversion ratio [2.0]:
    Form of distance matrix
             S : Square
             L : Lower-triangular
    Form [S]:
    Kimura
        5
    Alpha       0.0000  0.2997  0.7820  1.1716  1.4617
    Beta        0.2997  0.0000  0.3219  0.8997  0.5653
    Gamma       0.7820  0.3219  0.0000  1.4481  1.0726
    Delta       1.1716  0.8997  1.4481  0.0000  0.1679
    Epsilon     1.4617  0.5653  1.0726  0.1679  0.0000

## Command line arguments

       Mandatory qualifiers:
      [-msf]               seqset     File containing a sequence allignment
      [-outfile]           outfile    Output file name
       -method             list       Choose the method to use
       -ttratio            float      Transition/transversion ratio
       -matrix             list       Form

       Optional qualifiers (* if not always prompted):
       -categories         integer    Number of categories of substitution rates
    *  -[no]basefrequency  bool       Use empirical base frequencies
       -printinitial       bool       Print out the data at start of run
    *  -freqa              float      Frequency for A
    *  -freqc              float      Frequency for C
    *  -freqg              float      Frequency for G
    *  -freqt              float      Frequency for T/U

       Advanced qualifiers: (none)

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence allignment | Readable sequences | Required
[-outfile] (Parameter 2) | Output file name | Output file | ednadist.outfile

-method

Choose the method to use

Kimura | (Kimura 2-parameter distance)
JinNei | (Jin and Nei distance)
ML | (Maximum Likelihood distance)
Jukes | (Jukes-Cantor distance)

Kimura

-ttratio | Transition/transversion ratio | Number up to 100.000 | 2.0

-matrix

Form

S | (Square)
L | (Lower-triangular)

S

Optional qualifiers | Allowed values | Default
-categories | Number of categories of substitution rates | Any integer value | 1
-[no]basefrequency | Use empirical base frequencies | Yes/No | Yes
-printinitial | Print out the data at start of run | Yes/No | No
-freqa | Frequency for A | Number from 0.000 to 1.000 | 0.25
-freqc | Frequency for C | Number from 0.000 to 1.000 | 0.25
-freqg | Frequency for G | Number from 0.000 to 1.000 | 0.25
-freqt | Frequency for T/U | Number from 0.000 to 1.000 | 0.25
Advanced qualifiers | Allowed values | Default
(none)

## Data files

## Notes

Multiple sequences sets not implemented yet!.

## 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