EMBOSS: egendist

egendist

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Function

Conversion of PHYLIP's gendist

Description

EGENDIST - Embossified compute genetic distances from gene frequencies

Phylip gendist documentation.

Usage

Here is a sample session with egendist using the data :-

    5    10
2 2 2 2 2 2 2 2 2 2
European   0.2868 0.5684 0.4422 0.4286 0.3828 0.7285 0.6386 0.0205 0.8055 0.5043
African    0.1356 0.4840 0.0602 0.0397 0.5977 0.9675 0.9511 0.0600 0.7582 0.6207
Chinese    0.1628 0.5958 0.7298 1.0000 0.3811 0.7986 0.7782 0.0726 0.7482 0.7334
American   0.0144 0.6990 0.3280 0.7421 0.6606 0.8603 0.7924 0.0000 0.8086 0.8636
Australian 0.1211 0.2274 0.5821 1.0000 0.2018 0.9000 0.9837 0.0396 0.9097 0.2976


% egendist test

Genetic Distance Matrix program
Output file [egendist.outfile]: stdout
Distance methods
       Nei : Nei genetic distance
       Cav : Cavalli-Sforza chord measur
       Rey : Reynolds genetic distance
    prompt : "Choose the method to use
-method : enter list value [Nei]: 
    5
European    0.0000  0.0780  0.0807  0.0668  0.1030
African     0.0780  0.0000  0.2347  0.1050  0.2273
Chinese     0.0807  0.2347  0.0000  0.0539  0.0633
American    0.0668  0.1050  0.0539  0.0000  0.1348
Australian  0.1030  0.2273  0.0633  0.1348  0.0000

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-infile]            infile     data file
  [-outfile]           outfile    Output file name
   -method             list       (no help text) list value
*  -datasets           integer    How many data sets

   Optional qualifiers:
   -all                bool       Input file contains all alleles at each
                                  locus (else one)
   -lowertriangle      bool       Lower-triangular (else Square)
   -multsets           bool       Analyze multiple data sets
   -progress           bool       Print indications of progress of run

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

[-infile]
(Parameter 1) data file Input file Required

[-outfile]
(Parameter 2) Output file name Output file egendist.outfile

-method (no help text) list value
Nei (Nei genetic distance)
Cav (Cavalli-Sforza chord measur)
Rey (Reynolds genetic distance)
prompt ("Choose the method to use)
Nei

-datasets How many data sets Any integer value 0

Optional qualifiers Allowed values Default

-all Input file contains all alleles at each locus (else one) Yes/No No

-lowertriangle Lower-triangular (else Square) Yes/No No

-multsets Analyze multiple data sets 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

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.