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Sequence editor that can delete columns?

Nicolas_Galtier Nicolas_Galtier
Thu Feb 27 03:15:17 EST 1997

Brian Foley writes:
> 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 (Multiple Alignment Sequence Editor,
> D.Faulkner and J.Jurka, TIBS 13,321-322 (1988))
> 	In PHYLO_WIN (N. Galtier), 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.

I also suggest program SEAVIEW (M. Gouy), a powerful alignemnt
editor fully compatible with PHYLO_WIN and performing the above
task among many other including automatic alignment, interface
to dot-plot, etc...

SEAVIEW and PHYLO_WIN cope with the problem of undesired sites
by allowing (and storing) site selection, thus avoiding to duplicate
sequence files when a new set of sites is to be analysed. This
property also works for species groups. Selection is mouse-driven.
The very task you ask for (creating a new file after deleting columns)
is also performed by seaview, so that an interface with programs that
do not use our data-management format is ensured. Output file formats

Both programs run on Unix workstations and Linux PC compatible.
They are available by anonymous ftp to biom3.univ-lyon1.fr/pub/mol_phylogeny
or http://acnuc.univ-lyon1.fr/

Hope this helps.

Nicolas Galtier.
Laboratoire de Biometrie, Genetique et Biologie des Populations
Universite C.Bernard 

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