EMBOSS: ednadist

ednahist

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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

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.