kkitsch

 

Function

Fitch-Margoliash method with contemporary tips using kitsch

Description

kkitsch is fitch-Margoliash method with contemporary tips utilizing "kitsch" methods provided in PHYLIP web service.

Following block is a quotation from fkitsch included in PHYLIPNEW package. Estimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed. The Fitch-Margoliash criterion and other least squares criteria, or the Minimum Evolution criterion are possible. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with distances from DNA hybridization measurements, and with genetic distances computed from gene frequencies. PHYLIP web service is provided by National University of Singapore. Original web-service is located at the following URL:

http://bioportal.bic.nus.edu.sg/phylip/kitsch.html

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kkitsch is thus an interface of "runKitsch" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://www.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kkitsch

% kkitsch
Fitch-Margoliash method with contemporary tips using kitsch
Input file: sample.dat
Output file [55-110.kkitsch]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)
infile data file for kitsch Input file 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kkitsch
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

Input files for usage example

File: sample.dat


Output file format

Output files for usage example

File: sample.kkitsch

5 Populations

Fitch-Margoliash method with contemporary tips, version 3.57c

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

negative branch lengths not allowed




     +          
  +--4  
  !  +          
--1  
  !     +          
  !  +--2  
  +--3  +          
     !  
     +          


Sum of squares =      0.000

Average percent standard deviation =   0.00000

examined   73 trees

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

   4                  0.00000        0.00000
   1     4            0.00000        0.00000
   4                  0.00000        0.00000
   2                  0.00000        0.00000
   3     2            0.00000        0.00000
   2                  0.00000        0.00000
   1     3            0.00000        0.00000
   3                  0.00000        0.00000




Data files

None.

Notes

None.

References


   Felsenstein, J.,(1995) PHYLIP(Phylogeny Interface Package), version3.57c,
      Department of Genetics, University of Washington, Seattle.

   Swofford, D., et al.,(1996) Phylogenetic interface. In Hillis, D.M.,
      Moritz, C., and Mble, B.K.(eds), Molecular Systematics 2nd Edition,
      Sinauer Associates, Mss.


Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org) Institute for Advanced Biosciences, Keio University 252-8520 Japan

History

2009 - Written by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments