| ## 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,Alpha: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