kgendist

 

Function

Compute genetic distances from gene frequencies using gendist

Description

kgendist is compute genetic distances from gene frequencies utilizing "gendist" methods provided in PHYLIP web service.

Following block is a quotation from fgendist included in PHYLIPNEW package. Computes one of three different genetic distance formulas from gene frequency data. The formulas are Nei's genetic distance, the Cavalli-Sforza chord measure, and the genetic distance of Reynolds et. al. The former is appropriate for data in which new mutations occur in an infinite isoalleles neutral mutation model, the latter two for a model without mutation and with pure genetic drift. The distances are written to a file in a format appropriate for input to the distance matrix programs. 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/gendist.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. kgendistis thus an interface of "runGendist" 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 kgendist

% kgendist
Compute genetic distances from gene frequencies using gendist
Input file: sample.dat
Output file [55-110.kgendist]:
Jobid: kbws_12547145
***********

Command line arguments

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

Input file format

Input files for usage example

File: sample.dat






Output file format



Output files for usage example


File: sample.kgendist




5

European   0.0000  0.0780  0.0807  0.0668  0.3942

African    0.0780  0.0000  0.2347  0.1050  0.4856

Chinese    0.0807  0.2347  0.0000  0.0539  0.7243

American   0.0668  0.1050  0.0539  0.0000  0.6934

Australia  0.3942  0.4856  0.7243  0.6934  0.0000









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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