kpenny

 

Function

Penny algorithm, branch-and-bound using penny

Description

kpenny is penny algorithm, branch-and-bound utilizing "penny" methods provided in PHYLIP web service.

Following block is a quotation from fpenny included in PHYLIPNEW package. Finds all most parsimonious phylogenies for discrete-character data with two states, for the Wagner, Camin-Sokal, and mixed parsimony criteria using the branch-and-bound method of exact search. May be impractical (depending on the data) for more than 10-11 species. 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/penny.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. kpennyis thus an interface of "runPenny" 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 kpenny

% kpenny
Penny algorithm, branch-and-bound using penny
Input file: sample.dat
Output file [55-110.kpenny]:

Command line arguments

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

Input file format

Input files for usage example

File: sample.dat

      7    6
Alpha1    110110
Alpha2    110110
Beta1     110000
Beta2     110000
Gamma1    100110
Delta     001001
Epsilon   001110

Output file format

Output files for usage example

File: sample.kpenny

Penny algorithm, version 3.57c
 branch-and-bound to find all most parsimonious trees

Wagner parsimony method

                     


requires a total of              8.000

    3 trees in all found




  +-----------------
Alpha1   
  !  
  !        +--------
Alpha2   
--1        !  
  !  +-----4     +--
Epsilon  
  !  !     !  +--6  
  !  !     +--5  +--
Delta    
  +--2        !  
     !        +-----
Gamma1   
     !  
     !           +--
Beta2    
     +-----------3  
                 +--
Beta1    

  remember: this is an unrooted tree!




  +-----------------
Alpha1   
  !  
--1  +--------------
Alpha2   
  !  !  
  !  !           +--
Epsilon  
  +--2        +--6  
     !  +-----5  +--
Delta    
     !  !     !  
     +--4     +-----
Gamma1   
        !  
        !        +--
Beta2    
        +--------3  
                 +--
Beta1    

  remember: this is an unrooted tree!




  +-----------------
Alpha1   
  !  
  !           +-----
Alpha2   
--1  +--------2  
  !  !        !  +--
Beta2    
  !  !        +--3  
  +--4           +--
Beta1    
     !  
     !           +--
Epsilon  
     !        +--6  
     +--------5  +--
Delta    
              !  
              +-----
Gamma1   

  remember: this is an unrooted tree!




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