Sequence editor that can delete columns?

Brian Foley btf at t10.lanl.gov
Wed Feb 26 16:41:17 EST 1997


Robert J. Forster wrote:
> 
> I have quite a few alignments of 16S rRNA sequences from 
> which I would like to delete a highly variable region 
> before analysis.  

	I do this with MASE by writing the conserved 
regions to files, and then putting those files together.


MASE:
*****

MASE (Multiple Alignment Sequence Editor,
D.Faulkner and J.Jurka, TIBS 13,321-322 (1988))

    MASE (Multiple Alignment Sequence Editor):  
    to get a copy, contact through
    e-mail mbcrr.harvard.EDU; if that fails, 
    send a note to klose at darwin.bu.EDU.
    Professor Temple Smith, one of the authors 
    of the program, can be reached at
    Boston Univ./Bio-molecular Engineering 
    Resource Center/36 Cummington St.,
    3rd Floor/Boston, MA 02215; 
    tel. 617-353-7123; fax 617-353-7020.  
    MBCRR
    (Molecular Biology Computer Resource) 
    seems to be a facility shared by
    Boston Univ. and Harvard.

    Mase is maintained, at least in part, 
    by Jerzy Jurka, c/o Jim Mullins/
    Dept. of Microbiology and Immunology/Stanford 
    School of Medicine/Stanford,
    CA  94305; e-mail jurek at jmullins.Stanford.EDU.

	In PHYLO_WIN, one can select any region or 
regions of an alignment (including automatically 
selecting just first, second and/or third positions 
of each codon) for analysis.  PHYLO_WIN includes
neighbor-joining, maximum likelihood, etc. methods
of analysis.

    *****************************************************************
 *************** PHYLO_WIN LAST UPDATE : January 29, 1997
***************
    *****************************************************************


PHYLO_WIN is a graphic tool for molecular phylogenetic inferences.
Present version is phylo_win 1.2. 

phylo_win was compiled and run on the following platforms :

 - Sun (Solaris)
 - Sun (SunOS)
 - Silicon Graphics
 - IBM WorkStations running Unix
 - HP
 - DEC alpha

 - PC compatible using LINUX : distributed by Sicheritz Ponten Thomas E.
   at  http://skydancer.bmc.uu.se/~thomas  .
 - VMS : distributed by David Mathog at 
   http://seqaxp.bio.caltech.edu:8000/pub/SOFTWARE/phylo_win.zip

Nicolas Galtier                                                         
Laboratoire de biometrie, genetique et biologie des populations         
UMR CNRS 5558   e-mail : galtier at biomserv.univ-lyon1.fr
Universite C. Bernard - Lyon 1  
Tel    : +33 72-44-80-00 (41-43)
Fax    : +33 78-89-27-19 


-- 
 ____________________________________________________________________
|Brian T. Foley                btf at t10.lanl.gov                      |
|HIV Database                  (505) 665-1970                        |
|Los Alamos National Lab       http://hiv-web.lanl.gov/index.html    |
|Los Alamos, NM 87544  U.S.A.  http://retro.lanl.gov/~btf/home.html  |
|____________________________________________________________________|



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