kneighbor

 

Function

Phylogenies from distance matrix by N-J or UPGMA method using neighbor

Description

kneighbor is phylogenies from distance matrix by N-J or UPGMA method utilizing "neighbor" methods provided in PHYLIP web service.

Following block is a quotation from fneighbor included in PHYLIPNEW package. An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock. UPGMA does assume a clock. The branch lengths are not optimized by the least squares criterion but the methods are very fast and thus can handle much larger data sets. 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/neighbor.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. kneighboris thus an interface of "runNeighbor" 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 kneighbor

% kneighbor
Phylogenies from distance matrix by N-J or UPGMA method using neighbor
Input file: sample.dat
Output file [55-110.kneighbor]:
Jobid: kbws_12547145
***********

Command line arguments

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




5 Populations

Neighbor-Joining/UPGMA method version 3.57c


 Neighbor-joining method

 Negative branch lengths allowed


  +          
  !  
--3          
  !  
  !     +          
  !  +--1  
  +--2  +          
     !  
     +          


remember: this is an unrooted tree!

Between        And            Length
-------        ---            ------
   3                            0.00000
   3                            0.00000
   3             2              0.00000
   2             1              0.00000
   1                            0.00000
   1                            0.00000
   2                            0.00000











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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