EMBOSS: econtrast

econtrast

Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

Function

ECONTRAST -- Computes contrasts for comparative method

Description

Phylip contrast documentation.

Usage

Here is a sample session with econtrast for the data:-

    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

and the tree input file of

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


% econtrast test tree.test

Continuous character Contrasts
Output file [econtrast.outfile]: stdout

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

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-infile]            infile     input file
  [-treefile]          infile     input tree file
  [-outfile]           outfile    Output file name
*  -datasets           integer    How many data sets

   Optional qualifiers:
   -[no]corplusreg     bool       Print out correlations and regressions
   -multsets           bool       Analyze multiple data sets
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default

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

[-treefile]
(Parameter 2) input tree file Input file Required

[-outfile]
(Parameter 3) Output file name Output file econtrast.outfile

-datasets How many data sets Integer 1 or more 1

Optional qualifiers Allowed values Default

-[no]corplusreg Print out correlations and regressions Yes/No Yes

-multsets Analyze multiple data sets Yes/No No

-printdata Print out the data at start of run Yes/No No

-progress Print indications of progress of run Yes/No No

Advanced qualifiers Allowed values Default

(none)

Mandatory qualifiers	Allowed values	Default
[-infile] (Parameter 1)	input file	Input file	Required
[-treefile] (Parameter 2)	input tree file	Input file	Required
[-outfile] (Parameter 3)	Output file name	Output file	econtrast.outfile
-datasets	How many data sets	Integer 1 or more	1
Optional qualifiers	Allowed values	Default
-[no]corplusreg	Print out correlations and regressions	Yes/No	Yes
-multsets	Analyze multiple data sets	Yes/No	No
-printdata	Print out the data at start of run	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.