
                                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
