kdnamlk

Function

Description

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://soap.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]:
Jobid: kbws_12547145
***********

Command line arguments

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

Notes

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

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments