
	CLUSTAL X Multiple Sequence Alignment Program
                (version 1.4b, April 1997)


Clustal X provides a new window-based user interface to the ClustalW multiple
alignment program. It uses the Vibrant multi-platform user interface
development library, developed by the National Center for Biotechnology
Information (Bldg 38A, NIH 8600 Rockville Pike,Bethesda, MD 20894) as part of
their NCBI SOFTWARE DEVELOPEMENT TOOLKIT.
The toolkit is available by anonymous ftp from ncbi.nlm.nih.gov


Please e-mail bug reports/complaints/suggestions (polite if possible)
to Julie Thompson at julie@IGBMC.u-strasbg.fr
or Francois Jeanmougin at jeanmougin@IGBMC.u-strasbg.fr
 

New Features
------------

1. A subset of sequences in an alignment may be selected and realigned to a
profile made from the unselected sequences. This may be useful when trying to
align very divergent sequences which have been badly aligned in the initial
full multiple alignment.


2. A range of the sequence alignment can be selected for realignment. A new
phylogenetic guide tree is built based only on the residue range selected.
The selected residues are then aligned, and pasted back into the full sequence
alignment. This may be useful for aligning small sections of the alignment
which have been badly aligned in the full sequence alignment, or which have a
very different guide tree structure from the tree built using the full
sequences.


3. Clustal X provides a versatile coloring scheme for the sequence alignment
display. The sequences (or profiles) are colored automatically, when they are
loaded. Sequences can be colored either by assigning a color to specific
residues, or on the basis of an alignment consensus. In the latter case,
the alignment consensus is calculated automatically, and the residues in each
column are colored according to the consensus character assigned to the column.
In this way, for example, conserved hydrophylic or hydrophobic positions can
be highlighted.


4. An 'Alignment Quality Score' is plotted below the alignment. This is an
estimate of the conservation of each column in the alignment. Highly conserved
columns will have a high quality score, less conserved positions will be
marked by a low score.


5. 'Exceptional' residues in the alignment that cause the low quality scores
described above, can be highlighted. These can be expected to occur at a
moderate frequency in all the sequences because of their steady divergence
due to the natural processes of evolution. However, clustering of highlighted
residues is a strong indication of misalignment.
Occasionally, highlighted residues may also point to regions of some biological
significance.

6. Low-scoring segments in the alignment can be highlighted. The segments are
defined as those regions which score negatively in a forward and backward
summation of the alignment profile scores. See the online help for more
details.

7. The new GCG9 MSF,RSF formats are now recognised as input formats for
clustalx.  The alignments cannot be written out in these formats however.


Clustal W is a major re-write of the multiple alignment program Clustal V
(Ref: Higgins, Bleasby, and Fuchs (1991) CABIOS, 8, 189-191).

The major modifications are described in the paper:

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.


The code has been tested on UNIX (SGI, SUN, DIGITAL) and Macintosh. Compiled
executables are provided for these systems. If you wish to recompile the source
files, you will first need to install the NCBI toolkit on your machine.
Then, to compile the program on UNIX, edit the makefile to point to your NCBI
include and library files, and type:
  make -f makefile.sun    or    make -f makefile.sgi  or   make -f makefile.osf


To run the program, type clustalx. A window is displayed with a pull-down menu
bar which allow all functions to be selected and all alignment parameters
may be modified, if desired.


Documentation for ClustalW (clustalw.doc) is included in the directory. Online 
help is also available for most options of the program by selecting HELP from
the menu bar.
Help is also available on the WWW at

www-igbmc.u-strasbg.fr/BioInfo/ClustalW/
www.U.arizona.edu/~schluter/ClustalW/index.html


