econtrast

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Function

Description

Usage

% econtrast Continuous character contrasts Phylip continuous character frequency file: contrast.dat Phylip tree file: contrast.tree Analyze multiple data sets [N]: Phylip contrast program output file [econtrast.outfile]:

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

Command line arguments

Continuous character contrasts
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-infile]            infile     Phylip continuous character frequency file
  [-treefile]          infile     Phylip tree file
   -multsets           toggle     [N] Analyze multiple data sets
*  -datasets           integer    [1] How many data sets (Integer 1 or more)
  [-outfile]           outfile    [econtrast.outfile] Phylip contrast program
                                  output file

   Additional (Optional) qualifiers:
   -[no]corplusreg     boolean    [Y] Print out correlations and regressions
   -printdata          boolean    [N] Print out the data at start of run
   -progress           boolean    [N] Print indications of progress of run

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

   "-outfile" associated qualifiers
   -odirectory3        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 continuous character frequency file	Input file	Required
[-treefile] (Parameter 2)	infile	Phylip tree file	Input file	Required
-multsets	toggle	Analyze multiple data sets	Toggle value Yes/No	No
-datasets	integer	How many data sets	Integer 1 or more	1
[-outfile] (Parameter 3)	outfile	Phylip contrast program output file	Output file	econtrast.outfile
Additional (Optional) qualifiers
-[no]corplusreg	boolean	Print out correlations and regressions	Boolean value Yes/No	Yes
-printdata	boolean	Print out the data at start of run	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
-odirectory3 -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: contrast.dat

    5   2
Homo        4.09434  4.74493
Pongo       3.61092  3.33220
Macaca      2.37024  3.36730
Ateles      2.02815  2.89037
Galago     -1.46968  2.30259

File: contrast.tree

((((Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);

Output file format

Output files for usage example

File: econtrast.outfile

Contrasts (columns are different characters)
--------- -------- --- --------- -----------

   0.74593   2.17989
   1.58474   0.71761
   1.19293   0.86790
   3.35832   0.89706

Covariance matrix
---------- ------

    3.9423    1.7028
    1.7028    1.7062

Regressions (columns on rows)
----------- -------- -- -----

    1.0000    0.4319
    0.9980    1.0000

Correlations
------------

    1.0000    0.6566
    0.6566    1.0000

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

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