Restriction site maximum Likelihood method using restml


krestml is restriction site maximum Likelihood method utilizing "restml" methods provided in PHYLIP web service.

Following block is a quotation from frestml included in PHYLIPNEW package. Estimation of phylogenies by maximum likelihood using restriction sites data (not restriction fragments but presence/absence of individual sites). It employs the Jukes-Cantor symmetrical model of nucleotide change, which does not allow for differences of rate between transitions and transversions. This program is very slow. PHYLIP web service is provided by National University of Singapore. Original web-service is located at the following URL:

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. krestml is thus an interface of "runRestml" 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 for more information.


   Here is a sample session with krestml

% krestml
Restriction site maximum Likelihood method using restml
Input file: sample.dat
Output file [55-110.krestml]:

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
(Parameter 1)
infile data file for restml Input file 2
(Parameter 2)
outfile Output file name Output file <*>.krestml
Additional (Optional) qualifiers
Advanced (Unprompted) qualifiers

Input file format

Input files for usage example

File: sample.dat

     5   13   2
Alpha     ++-+-++--+++-
Beta      ++++--+--+++-
Gamma     -+--+-++-+-++
Delta     ++-+----++---
Epsilon   ++++----++---

Output file format

Output files for usage example

File: sample.krestml

Restriction site Maximum Likelihood method, version 3.57c

  Recognition sequences all 6 bases long

Sites absent from all species are assumed to have been omitted

Data files





   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.



Diagnostic Error Messages


Exit status

It always exits with a status of 0.

Known bugs


See also

Program name Description
seqret Reads and writes (returns) sequences


Kazuki Oshita (cory @ Institute for Advanced Biosciences, Keio University 252-8520 Japan


2009 - Written by Kazuki Oshita
Nov 2010 - little revision of this document

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.