EMBOSS: ekitsch

ekitsch

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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)

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

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.