kclique

 

Function

Largest clique program using clique

Description

kclique is largest clique program utilizing "clique" methods provided in PHYLIP web service.

Following block is a quotation from fclique included in PHYLIPNEW package. Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states. The largest clique (or all cliques within a given size range of the largest one) are found by a very fast branch and bound search method. The method does not allow for missing data. For such cases the T (Threshold) option of PARS or MIX may be a useful alternative. Compatibility methods are particular useful when some characters are of poor quality and the rest of good quality, but when it is not known in advance which ones are which. 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/clique.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. kclique is thus an interface of "runClique" 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 kclique

% kclique
Largest clique program using clique
Input (gapped) sequence(s): test.fasta
Output file [55-110.kclique]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)
infile standard input for discrete characters programs Input file 2
[-outfile]
(Parameter 2)
outfile Output file name Output file <*>.kclique
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.kclique

Largest clique program, version 3.57c




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