kdnadist

 

Function

Nucleic acid sequence Distance Matrix program using dnadist

Description

kdnadist is nucleic acid sequence Distance Matrix program utilizing "dnadist" methods provided in PHYLIP web service.

Following block is a quotation from fdnadist included in PHYLIPNEW package. Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, the F84 model used in DNAML, and the LogDet distance. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences. 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/dnadist.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. kdnadistis thus an interface of "runDnadist" 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 kdnadist

% kdnadist
Nucleic acid sequence Distance Matrix program using dnadist
Input (gapped) sequence(s): test.fasta
Output file [55-110.kdnadist]:


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 <*>.kdnadist
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)

Input file format

Input files for usage example

File: sample.dat

     4   13
Beta      AAGGUCGCCAAAC
Gamma     CAUUUCGUCACAA
Delta     GGUAUUUCGGCCU
Epsilon   GGGAUCUCGGCCC

Output file format

Output files for usage example

File: sample.kdnadist

4
Delta       0.0000  0.2806  0.5415  6.0600
Epsilon     0.2806  0.0000  0.6045  2.2833
Gamma       0.5415  0.6045  0.0000  1.0726
Beta        6.0600  2.2833  1.0726  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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