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://www.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]:

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.

Comments