kdollop

 

Function

Dollo and polymorphism parsimony algorithm using dollop

Description

kdollop is dollo and polymorphism parsimony algorithm utilizing "dollop" methods provided in PHYLIP web service.

Following block is a quotation from fdollop included in PHYLIPNEW package. Estimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0 and 1). Also reconstructs ancestral states and allows weighting of characters. Dollo parsimony is particularly appropriate for restriction sites data; with ancestor states specified as unknown it may be appropriate for restriction fragments data. 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/dollop.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. kdollopis thus an interface of "runDollop" 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 kdollop

% kdollop
Dollo and polymorphism parsimony algorithm using dollop
Input file: sample.dat
Output file [55-110.kdollop]:

Command line arguments

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

Dollo and polymorphism parsimony algorithm, version 3.57c

Dollo parsimony method


               


One most parsimonious tree found:




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


requires a total of      3.000





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