| ## EMBOSS: emix

# Program emix

## Function

Conversion of PHYLIP's mix

## Description

EMIX - Embossified mixed method parsimony

Phylip mix documentation.

## Usage

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

         5    6
    Alpha     110110
    Beta      110000
    Gamma     100110
    Delta     001001
    Epsilon   001110

    % emix test

    Mixed parsimony algorithm
    Output file [emix.outfile]: stdout
    Search for best tree [Y]:
    Method
           Wag : Wagner
           Cam : Camin-Sokal
           Mix : Mixed
        prompt : "Choose the method to use
    -method : enter list value [Wag]:
    Outgroup root [N]:
    Create a tree file [Y]:
    Treefile name [emix.treefile]:
    Wagner parsimony method

         4 trees in all found

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

      remember: this is an unrooted tree!

    requires a total of      9.000

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

      remember: this is an unrooted tree!

    requires a total of      9.000

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

      remember: this is an unrooted tree!

    requires a total of      9.000

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

      remember: this is an unrooted tree!

    requires a total of      9.000

    % more emix.treefile
    (((Epsilon,Gamma),(Delta,Beta)),Alpha)[0.2500];
    ((Gamma,((Epsilon,Delta),Beta)),Alpha)[0.2500];
    ((Epsilon,(Gamma,(Delta,Beta))),Alpha)[0.2500];
    ((Gamma,(Epsilon,(Delta,Beta))),Alpha)[0.2500];

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-infile]            infile     data file
      [-outfile]           outfile    Output file name
      [-[no]besttree]      bool       Search for best tree
       -method             list       (no help text) list value
    *  -randseed           integer    Random number seed (must be odd)
    *  -randtimes          integer    Number of times to jumble
       -og                 bool       Outgroup root
    *  -outgnum            integer    number of the outgroup
    *  -valthresh          float      threshold value
    *  -datasets           integer    How many data sets
      [-[no]trout]         bool       Create a tree file
    *  -treefile           outfile    Tree file name

       Optional qualifiers (* if not always prompted):
    *  -random             bool       Randomize input order of species
       -ancestral          bool       Use ancestral states in input file
       -multsets           bool       Analyze multiple data sets
       -printdata          bool       Print out the data at start of run
       -progress           bool       Print indications of progress of run
       -statesatnodes      bool       Print states at all nodes of tree
       -steps              bool       Print out steps in each character
       -[no]drawtree       bool       Draw tree

       Advanced qualifiers:
       -thresh             bool       Use Threshold parsimony

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-infile] (Parameter 1) | data file | Input file | Required
[-outfile] (Parameter 2) | Output file name | Output file | emix.outfile
[-[no]besttree] (Parameter 3) | Search for best tree | Yes/No | Yes
-method | (no help text) list value |
Wag | (Wagner)
Cam | (Camin-Sokal)
Mix | (Mixed)
prompt | ("Choose the method to use)
| Wag
-randseed | Random number seed (must be odd) | Any integer value | 0
-randtimes | Number of times to jumble | Any integer value | 0
-og | Outgroup root | Yes/No | No
-outgnum | number of the outgroup | Integer 1 or more | 1
-valthresh | threshold value | Number 1.000 or more | 1.0
-datasets | How many data sets | Any integer value | 0
[-[no]trout] (Parameter 4) | Create a tree file | Yes/No | Yes
-treefile | Tree file name | Output file | emix.treefile
Optional qualifiers | Allowed values | Default
-random | Randomize input order of species | Yes/No | No
-ancestral | Use ancestral states in input file | Yes/No | No
-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
-statesatnodes | Print states at all nodes of tree | Yes/No | No
-steps | Print out steps in each character | Yes/No | No
-[no]drawtree | Draw tree | Yes/No | Yes
Advanced qualifiers | Allowed values | Default
-thresh | Use Threshold parsimony | Yes/No | No

## 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