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
include MASE, CLUSTAL, PHYLIP, GCG, FASTA.
Both programs run on Unix workstations and Linux PC compatible.
They are available by anonymous ftp to biom3.univ-lyon1.fr/pub/mol_phylogeny
Hope this helps.
Laboratoire de Biometrie, Genetique et Biologie des Populations