kcontml

 

Function

Gene frequency and continuous character Maximum Likelihood using contml

Description

kcontml is gene frequency and continuous character Maximum Likelihood utilizing "contml" methods provided in PHYLIP web service.

Following block is a quotation from fcontml included in PHYLIPNEW package. Estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations. Does not assume a molecular clock. An alternative method of analyzing this data is to compute Nei's genetic distance and use one of the distance matrix programs. This program can also do maximum likelihood analysis of continuous characters that evolve by a Brownian Motion model, but it assumes that the characters evolve at equal rates and in an uncorrelated fashion, so that it does not take into account the usual correlations of characters. 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/contml.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. kcontml is thus an interface of "runContml" 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 kcontml

% kcontml
Gene frequency and continuous character Maximum Likelihood using contml
Input file: sample.dat
Output file [55-110.kcontml]:
Jobid: kbws_12547145
***********

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)		 infile data file for Contml Input file 2
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.kcontml
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.kcontml




5 Populations,   10 Loci

Continuous character Maximum Likelihood method version 3.57c


  +-----------------------------------------------------------
Australia
  !  
  !  +--------
African  
--3--1  
  !  !   +-
American 
  !  +---2  
  !      +----
Chinese  
  !  
  +
European 


remember: this is an unrooted tree!

Ln Likelihood =    22.00022

examined   15 trees

Between     And             Length      Approx. Confidence Limits
-------     ---             ------      ------- ---------- ------
  3       
Australia        0.59063   (     0.19034,     1.20969)
  3          1              0.00641   (    -0.01944,     0.04640)
  1       
African          0.08446   (     0.02336,     0.17896)
  1          2              0.03614   (    -0.00236,     0.09568)
  2       
American         0.02029   (    -0.00942,     0.06625)
  2       
Chinese          0.05347   (     0.00795,     0.12387)
  3       
European         0.00000   (    -0.02428,     0.03756)











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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