| ## EMBOSS: ekitsch

# Program ekitsch

## Function

Conversion of PHYLIP's kitsch

## Description

EKITSCH -- Embossified Fitch-Margoliash and Least Squares Methods with Evolutionary Clock

Phylip kitsch documentation.

## Usage

Here is a sample session with ekitsch 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

    % ekitsch test

    Fitch-Margoliash method with contemporary tips
    Output file [ekitsch.outfile]: stdout
    Search for best tree [Y]:
    Treefile name [ekitsch.treefile]:

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

    negative branch lengths not allowed

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

    Sum of squares =      0.000

    examined   76 trees

    From    To           Length          Time
    ----    --           ------          ----

       4  Epsilon         0.50000        1.50000
       3     4            1.00000        1.00000
       4  Delta           0.50000        1.50000
       1  Beta            0.50000        1.50000
       2     1            0.50000        1.00000
       1  Alpha           0.50000        1.50000
       3     2            0.50000        0.50000
       2  Gamma           1.00000        1.50000

    % more ekitsch.treefile
    (Epsilon:0.50000,Delta:0.50000):1.00000,((Beta:0.50000,
    Alpha:0.50000):0.50000,Gamma:1.00000):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
    *  -datasets           integer    How many data sets
       -treefile           outfile    Tree file name

       Optional qualifiers (* if not always prompted):
       -power              float      Power
       -negbranch          bool       Negative branch lengths allowed
    *  -random             bool       Randomize input order of species
       -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 | ekitsch.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
-datasets | How many data sets | Any integer value | 0
-treefile | Tree file name | Output file | ekitsch.treefile
Optional qualifiers | Allowed values | Default
-power | Power | Any integer value | 3.0
-negbranch | Negative branch lengths allowed | Yes/No | No
-random | Randomize input order of species | 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