kfitch

 

Function

Fitch-Margoliash and Least-Squares Distance Methods using fitch

Description

kfitch is fitch-Margoliash and Least-Squares Distance Methods utilizing "fitch" methods provided in PHYLIP web service.

Following block is a quotation from ffitch included in PHYLIPNEW package. Estimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria, or the Minimum Evolution distance matrix method. Does not assume an evolutionary clock. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with 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/fitch.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. kfitchis thus an interface of "runFitch" 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 kfitch

% kfitch
Fitch-Margoliash and Least-Squares Distance Methods using fitch
Input file: sample.dat
Output file [55-110.kfitch]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)
infile data file for fitch Input file 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kfitch
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.kfitch

5 Populations

Fitch-Margoliash method version 3.57c

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

Negative branch lengths not allowed


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


remember: this is an unrooted tree!

Sum of squares =     0.00000

Average percent standard deviation =     0.00000

examined   15 trees

Between        And            Length
-------        ---            ------
   3                            0.00000
   3             2              0.00000
   2                            0.00000
   2             1              0.00000
   1                            0.00000
   1                            0.00000
   3                            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