EMBOSS: ednapars

| ## EMBOSS: ednapars

# Program ednapars

## Function

Conversion of PHYLIP's dnapars

## Description

EDNAPARS -- Embossified DNA Parsimony Program

Phylip dnapars documentation.

## Usage

Here is a sample session with ednapars using test data:-

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

    % ednapars test

    DNA parsimony algorithm
    Output file [ednapars.outfile]: stdout
    Randomize input order of species [N]:
    Create a tree file [Y]:
    Output treefile name [ednapars.treefile]:

    One most parsimonious tree found:

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

      remember: this is an unrooted tree!

    requires a total of     19.000

    % more more ednapars.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
    *  -random             bool       Randomize input order of species
    *  -randseed           integer    Random number seed (must be odd)
    *  -randtimes          integer    How many times to randomise
    *  -outgnum            integer    number of the outgroup
    *  -valthresh          float      threshold value
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name

       Optional qualifiers:
       -[no]besttree       bool       Search for best tree
       -og                 bool       Outgroup root
       -printdata          bool       Print out the data at start of run
       -progress           bool       Print indications of progress of run
       -steps              bool       Print out steps in each site
       -seqatnodes         bool       Print sequences at all nodes of tree
       -[no]drawtree       bool       Draw tree

       Advanced qualifiers:
       -thresh             bool       Use Threshold parsimony

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence allignment | Readable sequences | Required
[-outfile] (Parameter 2) | Output file name | Output file | ednapars.outfile
-random | Randomize input order of species | Yes/No | No
-randseed | Random number seed (must be odd) | Any integer value | 3
-randtimes | How many times to randomise | Any integer value | 3
-outgnum | number of the outgroup | Integer 1 or more | 1
-valthresh | threshold value | Number 1.000 or more | 1.0
[-[no]trout] (Parameter 3) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | ednapars.treefile
Optional qualifiers | Allowed values | Default
-[no]besttree | Search for best tree | Yes/No | Yes
-og | Outgroup root | 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
-steps | Print out steps in each site | Yes/No | No
-seqatnodes | Print sequences at all nodes of tree | Yes/No | No
-[no]drawtree | Draw tree | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
-thresh | Use Threshold parsimony | Yes/No | No

## Data files

## Notes

Multiple sequences sets not implemented yet!.

## 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