EMBOSS: ednacomp

| ## EMBOSS: ednacomp

# Program ednacomp

## Function

Conversion of PHYLIP's dnacomp

## Description

EDNACOMP -- Embossified DNA Compatibility Program

Phylip dnacomp documentation.

## Usage

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

        5   13
    Alpha     AACGUGGCCAAAU
    Beta      AAGGUCGCCAAAC
    Gamma     CAUUUCGUCACAA
    Delta     GGUAUUUCGGCCU
    Epsilon   GGGAUCUCGGCCC

    % ednacomp test

    DNA compatibility algorithm
    Output file [ednacomp.outfile]: stdout
    Create a tree file [Y]:
    Treefile name [ednacomp.treefile]:
    Outgroup root [N]:

    One most parsimonious tree found:

               +--Epsilon
            +--4
         +--3  +--Delta
         !  !
      +--2  +-----Gamma
      !  !
    --1  +--------Beta
      !
      +-----------Alpha

      remember: this is an unrooted tree!

    total number of compatible sites is       11.0

    % more ednacomp.treefile
    ((((Epsilon,Delta),Gamma),Beta),Alpha);

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-msf]               seqset     File containing a sequence allignment
      [-outfile]           outfile    Output file name
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name
       -og                 bool       Outgroup root
    *  -outgnum            integer    number of the outgroup
    *  -randseed           integer    Random number seed (must be odd)
    *  -randtimes          integer    Number of times to jumble

       Optional qualifiers:
       -[no]drawtree       bool       Draw tree
       -printdata          bool       Print out the data at start of run
       -progress           bool       Print indications of progress of run
       -stepoutput         bool       Print steps & compatibility at sites
       -allnodes           bool       Print sequences at all nodes of tree
       -random             bool       Randomize input order of species

       Advanced qualifiers: (none)

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence allignment | Readable sequences | Required
[-outfile] (Parameter 2) | Output file name | Output file | ednacomp.outfile
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | ednacomp.treefile
-og | Outgroup root | Yes/No | No
-outgnum | number of the outgroup | Integer 1 or more | 1
-randseed | Random number seed (must be odd) | Any integer value | 0
-randtimes | Number of times to jumble | Any integer value | 0
Optional qualifiers | Allowed values | Default
-[no]drawtree | Draw tree | Yes/No | Yes
-printdata | Print out the data at start of run | Yes/No | No
-progress | Print indications of progress of run | Yes/No | No
-stepoutput | Print steps & compatibility at sites | Yes/No | No
-allnodes | Print sequences at all nodes of tree | Yes/No | No
-random | Randomize input order of species | 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