EMBOSS: econtrast

| ## EMBOSS: econtrast

# Program econtrast

Conversion of PHYLIP's contrast

## 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)

## Input file format

## Output file format

## Data files

## Notes

## References

## Warnings

## Diagnostics

## Exit status

## Known bugs

## See also

## 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.

## Priority

## Target users

## Comments