readme_x

经典生物信息学多序列比对工具clustalw

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	        CLUSTAL X Multiple Sequence Alignment Program
                         (version 1.83, Feb 2003)

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This README contains notes on version CHANGES and help with INSTALLATION

Clustal X provides a new window-based user interface to the Clustal W 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 [e-mail]
	or Toby Gibson at [e-mail]
 
 
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            POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W and X

Clustal W and X are freely available to the user community. However, Clustal W
is increasingly being distributed as part of commercial sequence analysis
packages. To help us safeguard future maintenance and development, commercial
distributors of Clustal X must take out a non-exclusive licence. Anyone
wishing to commercially distribute version 1.81 of Clustal X should contact the
authors unless they have previously taken out a licence. 

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Changes since CLUSTAL X Version 1.82
------------------------------------

1. The FASTA format has been added to the list of alignment output options.

2. It is now possible to save the residue ranges (appended after the sequence
names) when saving a specified range of the alignment.

3. The efficiency of  the neighour-joining algorithm has been improved. This
work was done by Tadashi Koike at the Center for Information Biology and DNA Data 
Bank of Japan and FUJITSU Limited.

Some example speedups are given below : (timings on a SPARC64 CPU)

No. of sequences	original NJ	new NJ
     200		0' 12"		0.1"
     500		9' 19"		1.4"
     1000		XXXX		0' 31"


Changes since CLUSTAL X Version 1.8
-----------------------------------

1. ClustalX now returns error codes for some common errors when exiting. This
may be useful for people who run clustalx automatically from within a script.
Error codes are:
        1       bad command line option
        2       cannot open sequence file
        3       wrong format in sequence file
        4       sequence file contains only 1 sequence (for multiple alignments)

2. Alignments can now be saved in Nexus format, for compatibility with PAUP,
MacClade etc. For a description of the Nexus format, see:
Maddison, D. R., D. L. Swofford and W. P. Maddison.  1997.
NEXUS: an extensible file format for systematic information.
Systematic Biology 46:590-621.

3. Phylogenetic trees can also be saved in nexus format.

4. A bug causing ClustalX to crash during cut-and-paste operations has been fixed.

5. A bug on PC systems, causing an error message when writing to files with
space characters in the filename has been fixed.

6. The Quality Curve is now displayed as a bar chart, instead of a line plot.
(Thanks to Michele Clamp, [e-mail], who used this format in the JalView
editor.)

7. A bug in the 'Save Profile' option, causing the default profile filename to
be lost has been fixed.

8. A ClustalX icon has been designed for MAC and PC systems.


Changes since CLUSTAL X Version 1.65b
-------------------------------------

1. Some work has been done to automatically select the optimal parameters
depending on the set of sequences to be aligned. The Gonnet series of residue
comparison matrices are now used by default. The Blosum series remains as an
option. The default gap extension penalty for proteins has been changed to 0.2
(was 0.05).The 'delay divergent sequences' option has been changed to 30%
residue identity (was 40%).

2. The default parameters used when the 'Negative matrix' option is selected
have been optimised. This option may help when the sequences to be aligned are
not superposable over their whole lengths (e.g. in the presence of N/C terminal
extensions).

3. An option has been added to save the quality scores displayed underneath the
sequence window to a text file.

4. The 'Hide Low-scoring segments' option has been moved from the Low-scoring
parameter window to the Quality menu, and has been changed to 'Show Low-scoring
segments'.

5. An option has been added to allow the user to search for a string in the
sequences.

6. An option has been added to the postscript output to print on US Letter size
paper.

7. A bug in the display of the message at the bottom of the window causing the
text to disappear when the window was resized has been fixed.

8. The font for the Help window as been changed to Courier.

9. A bug in the calculation of phylogenetic trees for 2 sequences has been
fixed.

10. A command line option has been added to turn off the sequence weighting
calculation.

11. The phylogenetic tree calculation now ignores any ambiguity codes in the
sequences.

12.  A bug in the memory access during the calculation of profiles has been
fixed. (Thanks to Haruna Cofer at SGI).

13. A bug has been fixed in the 'transition weight' option for nucleic acid
sequences. (Thanks to Chanan Rubin at Compugen).

14. An option has been added to allow the user to read in a series of residue
comparison matrices from a file.

15. The MSF output file format has been changed. The sequence weights
calculated by ClustalX are now included in the header. 

16. Two bugs in the FAST/APPROXIMATE pairwise alignments have been fixed. One
involved the alignment of new sequences to an existing profile using the fast
pairwise alignment option; the second was caused by changing the default
options for the fast pairwise alignments.

17. 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.

18. Several bugs affecting use of secondary structure masks in Clustal X (but
not in Clustal W) have been fixed. 


Changes since Version 1.5b
--------------------------

1. The window displayed under MS Windows has previously been a fixed size. The
window can now be resized by dragging the window frame.

2. An option has been added to read in a series of comparison matrices from a
file. This option is only applicable for protein sequences. For details of
the file format, see the on-line documentation.

3. A new DNA comparison matrix has been added. This is the default scoring 
matrix used by BESTFIT for the comparison of nucleic acid sequences. X's and N's
are treated as matches to any IUB ambiguity symbol. All matches score 1.9; all
mismatches for IUB symbols score 0.
The previous system used by ClustalW, in which matches score 1.0 and mismatches
score 0 remains as an option. All matches for IUB symbols will also score 0.

4. You can now read a comparison matrix for DNA sequences from a file. The
matrix file should be in the same format as for the Blast program.

5. The 'Reset gaps before alignment' has been changed to 'Reset new gaps
before alignments'. A new option 'Reset ALL gaps before alignment' has been
added.
RESET NEW GAPS BEFORE ALIGNMENT will remove any new gaps introduced into the
sequences during multiple alignment if you wish to change the parameters and
try again.
RESET ALL GAPS BEFORE ALIGNMENT will remove all gaps in the sequences including
gaps which were read in from the sequence input file. 
 
6. The 'Realign Residue Range' option has been changed. By default, gap
opening and extension penalties are now applied to the ends of the alignment
range in order to penalise terminal gaps. If the REALIGN SEGMENT END GAP
PENALTIES option is switched off, gaps can be introduced at the ends of the
residue range at no cost.

7. The MSF output file format has been changed. The sequence weights calculated
by ClustalX are now included in the header.

8. Two bugs in the FAST/APPROXIMATE pairwise alignments have been fixed. One
involved the alignment of new sequences to an existing profile using the
fast pairwise alignment option; the second was caused by changing the default
options for the fast pairwise alignments.