readme_x

经典生物信息学多序列比对工具clustalw

9. A bug in the postscript output file has been fixed. The residue numbers
printed at the right hand side of the alignment were not always correct.

10. A bug in the alignment of a small number of sequences has been fixed.
Previously a Guide Tree was not calculated for less than 4 sequences.

11. A bug which occurred after frequent cut-and-paste operations has been
fixed.

12. A new file called clustalx.html contains an html'ised version of the
on-line help. The file can be viewed using a World Wide Web viewer, such as
Netscape.


New Features since ClustalW
---------------------------

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.

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 Clustal X by selecting HELP from
the menu bar.

Help is also available on the WWW at

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


INSTALLATION    (for Unix, PC and MAC)
------------

UNIX
----

Executables are provided in the appropriate archives for Digital UNIX 4.0 on
Alphas, Sun OS 5.6, Silicon Graphics IRIX 6.2 and LINUX (libc6 must be
installed). If you wish to run on another platform, you will need to recompile
Clustal X for yourself.

The executable file clustalx should be copied to one of the directories
specified in your PATH environment variable. The files called *.par and
clustalx_help should also be copied to the same directory.

Recompiling ClustalX:

First of all, you need the NCBI Vibrant toolkit installed on your machine. If
this is not already done, you can get the toolkit by anonymous ftp to
ncbi.nlm.nih.gov.
You should then copy one of the makefiles supplied in the unix archives to
'makefile' and edit it, changing the NCBI_INC and NCBI_LIB paths for your
system.

You make the program with:
make -f makefile

This produces the executable file clustalx. You can then proceed with the 
installation as described above.


MS WINDOWS
----------

We supply an executable file (clustalx.exe) which will run under MS Windows 
(32 bit). The directory containing the executable (plus the files named *.par,
and clustalx.hlp) should be added to your path defined in the autoexec.bat
file.


Recompiling ClustalX:

First of all, you need the NCBI Vibrant toolkit installed on your machine. If
this is not already done, you can get the toolkit by anonymous ftp to
ncbi.nlm.nih.gov.

A makefile is supplied which can be used as a guide for recompiling the
ClustalX source code. You will need to edit it for your system. In 
particular the NCBI_INC and NCBI_LIB paths should point to your installation.


MAC
---

An executable program called clustalx is supplied for Power Macintoshes.
For 68K machines, you will need to recompile the code yourself. The 
program may need up to 10m of memory to run depending on the number and
length of your sequences. The memory allocation can be adjusted with the
Get Info (%I) command from the Finder if you have problems. Just double click 
the executable file name or icon and off you go (we hope). The files *.par and
clustalx_help should be stored in the same directory as the clustalx program.

Recompiling ClustalX:

First of all, you need the NCBI Vibrant toolkit installed on your machine. If
this is not already done, you can get the toolkit by anonymous ftp to
ncbi.nlm.nih.gov.

We used the Metroworks Codewarrior C compiler to compile the ClustalX files,
but another ANSI C compiler should work. You need to compile all the *.c
files supplied in the archive, then link them together with the NCBI Toolkit
libraries 'ncbi' and 'vibrant'.


                            CLUSTAL REFERENCES
                            ------------------

Details of algorithms, implementation and useful tips on usage of Clustal
programs can be found in the following publications:

Jeanmougin,F., Thompson,J.D., Gouy,M., Higgins,D.G. and Gibson,T.J. (1998)
Multiple sequence alignment with Clustal X. Trends Biochem Sci, 23, 403-5.

Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997)
The ClustalX windows interface: flexible strategies for multiple sequence 
alignment aided by quality analysis tools. Nucleic Acids Research, 25:4876-4882.

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

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., Bleasby,A.J. and Fuchs,R. (1992) CLUSTAL V: improved software for
multiple sequence alignment. CABIOS 8,189-191.

Higgins,D.G. and Sharp,P.M. (1989) Fast and sensitive multiple sequence
alignments on a microcomputer. CABIOS 5,151-153.

Higgins,D.G. and Sharp,P.M. (1988) CLUSTAL: a package for performing multiple
sequence alignment on a microcomputer. Gene 73,237-244.