egendist

Wiki

Please help by correcting and extending the Wiki pages.

Function

Description

Phylip gendist documentation.

Usage

% egendist Genetic distance matrix program Phylip gendist program input file: gendist.dat Distance methods Nei : Nei genetic distance Cav : Cavalli-Sforza chord measure Rey : Reynolds genetic distance Choose the method to use [Nei]: Phylip gendist program output file [egendist.outfile]:

Go to the input files for this example
Go to the output files for this example

Command line arguments

Genetic distance matrix program
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-infile]            infile     Phylip gendist program input file
*  -datasets           integer    [0] How many data sets (Any integer value)
   -method             menu       [Nei] Choose the method to use (Values: Nei
                                  (Nei genetic distance); Cav (Cavalli-Sforza
                                  chord measure); Rey (Reynolds genetic
                                  distance))
  [-outfile]           outfile    [egendist.outfile] Phylip gendist program
                                  output file

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

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-infile] (Parameter 1)	infile	Phylip gendist program input file	Input file	Required
-datasets	integer	How many data sets	Any integer value	0
-method	list	Choose the method to use	Nei (Nei genetic distance) Cav (Cavalli-Sforza chord measure) Rey (Reynolds genetic distance)	Nei
[-outfile] (Parameter 2)	outfile	Phylip gendist program output file	Output file	egendist.outfile
Additional (Optional) qualifiers
-lowertriangle	boolean	Lower-triangular (else Square)	Boolean value Yes/No	No
-multsets	toggle	Analyze multiple data sets	Toggle value Yes/No	No
-all	boolean	Input file contains all alleles at each locus (else one)	Boolean value Yes/No	No
-progress	boolean	Print indications of progress of run	Boolean value Yes/No	No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory2 -odirectory_outfile	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

Input files for usage example

File: gendist.dat

    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

Output file format

Output files for usage example

File: egendist.outfile

    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

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

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.

History

Target users

Comments

None