kdnamlk

 

Function

Estimates nucleotide phylogeny by maximum likelihood using dnamlk

Description

kdnamlk is estimates nucleotide phylogeny by maximum likelihood utilizing "dnamlk" methods provided in PHYLIP web service.

Following block is a quotation from fdnamlk included in PHYLIPNEW package. Same as DNAML but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made. Estimates phylogenies from nucleotide sequences by maximum likelihood. The model employed allows for unequal expected frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different (prespecified) rates of change in different categories of sites, and also use of a Hidden Markov model of rates, with the program inferring which sites have which rates. This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites. 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/dnamlk.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. kdnamlkis thus an interface of "runDnamlk" 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 kdnamlk

% kdnamlk
Estimates nucleotide phylogeny by maximum likelihood using dnamlk
Input (gapped) sequence(s): test.fasta
Output file [55-110.kdnamlk]:

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 <*>.kdnamlk
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.kdnamlk

4 Species,   15 Sites

Nucleic acid sequence
   Maximum Likelihood method with molecular clock, version 3.57c


Empirical Base Frequencies:

   A       0.21154
   C       0.30769
   G       0.25000
  T(U)     0.23077

Transition/transversion ratio =   2.000000

(Transition/transversion parameter =   1.514095)





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


Ln Likelihood =   -59.92907

 Ancestor      Node      Node Time     Length
 --------      ----      ---- ----     ------
 root            3      
   3          Beta         6.47680     6.47680
   3             2         6.19305     6.19305
   2             1         6.33023     0.13718
   1          Epsilon      6.47680     0.14657
   1          Delta        6.47680     0.14657
   2          Gamma        6.47680     0.28376





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