kmix

 

Function

Mixed parsimony algorithm using mix

Description

kmix is mixed parsimony algorithm utilizing "mix" methods provided in PHYLIP web service.

Following block is a quotation from fmix included in PHYLIPNEW package. Estimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1). Allows use of the Wagner parsimony method, the Camin-Sokal parsimony method, or arbitrary mixtures of these. Also reconstructs ancestral states and allows weighting of characters (does not infer branch lengths). 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/mix.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. kmixis thus an interface of "runMix" 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://soap.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kmix

% kmix
Mixed parsimony algorithm using mix
Input file: sample.dat
Output file [55-110.kmix]:
Jobid: kbws_12547145
***********

Command line arguments

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

Input file format

Input files for usage example

File: sample.dat

       5    6
Alpha     110110
Beta      110000
Gamma     100110
Delta     001001
Epsilon   001110

Output file format

Output files for usage example

File: sample.kmix

Mixed parsimony algorithm, version 3.57c

Wagner parsimony method


               


     4 trees in all found




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

  remember: this is an unrooted tree!


requires a total of      9.000





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

  remember: this is an unrooted tree!


requires a total of      9.000





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

  remember: this is an unrooted tree!


requires a total of      9.000





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

  remember: this is an unrooted tree!


requires a total of      9.000

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