
                               EMBOSS: efitch
     _________________________________________________________________
   
                                Program efitch
                                       
Function

   Conversion of PHYLIP's fitch
   
Description

   EFITCH -- Embossified Fitch-Margoliash and Least-Squares Distance
   Methods
   
   Phylip fitch documentation.
   
Usage

   Here is a sample session with efitch using the data:-
    5
Alpha      0.000 1.000 2.000 3.000 3.000
Beta       1.000 0.000 2.000 3.000 3.000
Gamma      2.000 2.000 0.000 3.000 3.000
Delta      3.000 3.000 3.000 0.000 1.000
Epsilon    3.000 3.000 3.000 1.000 0.000


% efitch test

Fitch-Margoliash and Least-Squares Distance Methods
Output file [efitch.outfile]: stdout
Search for best tree [Y]:
Outgroup root [N]:
Create a tree file [Y]:
Treefile name [efitch.treefile]:

   5 Populations
                  __ __             2
                  \  \   (Obs - Exp)
Sum of squares =  /_ /_  ------------
                                3
                   i  j      Obs

Negative branch lengths not allowed


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


remember: this is an unrooted tree!

Sum of squares =     0.00000

examined   15 trees

Between        And            Length
-------        ---            ------
   1          Beta              0.50000
   1             2              0.50000
   2             3              1.50000
   3          Epsilon           0.50000
   3          Delta             0.50000
   2          Gamma             1.00000
   1          Alpha             0.50000





% more efitch.treefile
(Beta:0.50000,((Epsilon:0.50000,Delta:0.50000):1.50000,Gamma:1.00000):0.50000,A
lpha:0.50000);

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
*  -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
*  -datasets           integer    How many data sets
  [-[no]trout]         bool       Create a tree file
*  -treefile           outfile    Tree file name

   Optional qualifiers (* if not always prompted):
*  -length             bool       Use lengths from user trees
   -power              float      Power
   -negbranch          bool       Negative branch lengths allowed
*  -random             bool       Randomize input order of species
*  -global             bool       Global rearrangements
   -lt                 bool       Lower-triangular data matrix
   -ut                 bool       Upper-triangular data matrix
   -replicates         bool       Subreplicates
   -multsets           bool       Analyze multiple data sets
   -printdata          bool       Print out the data at start of run
   -progress           bool       Print indications of progress of run
   -[no]drawtree       bool       Draw tree

   Advanced qualifiers: (none)
   
   Mandatory qualifiers Allowed values Default
   [-infile]
   (Parameter 1) data file Input file Required
   [-outfile]
   (Parameter 2) Output file name Output file efitch.outfile
   [-[no]besttree]
   (Parameter 3) Search for best tree Yes/No Yes
   -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
   -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 <sequence>.efitch
   Optional qualifiers Allowed values Default
   -length Use lengths from user trees Yes/No No
   -power Power Any integer value 3.0
   -negbranch Negative branch lengths allowed Yes/No No
   -random Randomize input order of species Yes/No No
   -global Global rearrangements Yes/No No
   -lt Lower-triangular data matrix Yes/No No
   -ut Upper-triangular data matrix Yes/No No
   -replicates Subreplicates 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
   -[no]drawtree Draw tree Yes/No Yes
   Advanced qualifiers Allowed values Default
   (none)
   
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
