kprotpars

 

Function

Protein parsimony algorithm using protpars

Description

kprotpars is protein parsimony algorithm utilizing "protpars" methods provided in PHYLIP web service.

Following block is a quotation from fprotpars included in PHYLIPNEW package. Estimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished. 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/protpars.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. kprotpars is thus an interface of "runProtpars" 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 kprotpars

% kprotpars
Protein parsimony algorithm using protpars
Input (gapped) sequence(s): test.fasta
Output file [55-110.kprotpars]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)
seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kprotpars
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

Input files for usage example

File: sample.dat

       5    10
Alpha     ABCDEFGHIK
Beta      AB--EFGHIK
Gamma     ?BCDSFG.??
Delta     CIKDEFGHIK
Epsilon   DIKDEFGHIK

Output file format

Output files for usage example

File: sample.kprotpars

Protein parsimony algorithm, version 3.57c



     3 trees in all found




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

  remember: this is an unrooted tree!


requires a total of     17.000




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

  remember: this is an unrooted tree!


requires a total of     17.000




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

  remember: this is an unrooted tree!


requires a total of     17.000




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.

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