ClustalW 1.7 new release

Toby Gibson gibson
Fri Jun 27 09:54:36 EST 1997


Dear All,

We are pleased to announce Version 1.7 of the Clustal W Multiple Sequence
Alignment Program.

Clustal W was published in:

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W:
improving the sensitivity of progressive multiple sequence alignment
through sequence weighting, positions-specific gap penalties and weight
matrix choice.  Nucleic Acids Research, 22:4673-4680.

Higgins, D. G., Thompson, J. D. and Gibson, T. J. (1996) Using CLUSTAL
for multiple sequence alignments. Methods Enzymol., 266, 383-402.


The main updates are:

     -   There is now no limit on the number or length of sequences which
     can be aligned (except the amount of memory in your machine of
     course!)

     -   Profile to profile alignments have been improved.

     -   The addition of new sequences to existing alignments has been
     improved.

     -   The treatment of sequences of unequal length has been improved.

     -   A bug in the alignment algorithm has been fixed. This
     occasionally caused new gaps to be opened a few residues away from
     the optimal position.

     -   The alignment of DNA sequences now offers a new hard-coded
     matrix, as well as the identity matrix used previously. IUB
     ambiguity symbols are no longer replaced by 'N'. You can now load
     your own favorite DNA comparison matrix from a Blast format file.

     -   The RSF sequence alignment file format used by GCG Version 9
     can now be read.

     -   By popular demand, sequence numbering is now available in
     Clustal format output.

     -   Also by popular demand, sequence names can be longer than 10
     chars. (Longer names are incompatible with the PHYLIP package).

The software is available by anonymous ftp to one of:

ftp.embl-heidelberg.de
    unix   pub/software/unix/clustalw.17.tar.Z  (compressed tar archive)
    vms    pub/software/vms/clustalw_17.uue     (uuencoded ZIP archive)
    mac    pub/software/mac/clustalw.17.sea.hqx (self extracting
archive/binhex)     PC     pub/software/dos/clustalw17$.exe     (self
extracting ZIP archive)

        Transfer the unix and PC versions in BINARY mode; transfer the vms
        and mac versions as ASCII!  The MAC and PC versions include
        executables.

ftp-igbmc.u-strasbg.fr   in directory /ftp/pub/ClustalW

ftp.ebi.ac.uk                (coming soon!!)

Versions are available for UNIX (tested on SGI, SUN), VMS, PC and Macintosh.
Included in the release are: all source code, updated documentation,
compiled executables (except for UNIX), and a README file giving full
details of the changes since Version 1.6.

ATTENTION SOFTWARE DEVELOPERS!! Please take note of the new features and to
the modifications affecting the alignment and tree output formats.

If you have any questions or comments, please contact one of:

Julie Thompson at julie at IGBMC.u-strasbg.fr
Toby Gibson    at Gibson at EMBL-Heidelberg.DE
Des Higgins    at D.Higgins at ucc.ie


******************************************************************************

                  POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W


Clustal W is freely available to the user community. However, we have had
several years of instability with regard to Clustal W maintenance and
development. Clustal W is now being distributed in a number of commercial
packages. To help us safeguard future maintenance and development,
commercial distributors of Clustal W are requested to donate a grant to the
Clustal W authors which will be spent on Clustal W-related development.
Anyone wishing to distribute version 1.7 of Clustal W should contact the
authors.

******************************************************************************



-- 
Julie Thompson, Toby Gibson, Des Higgins





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