clustalw使用方法

README for Clustal W version 1.6 March 1996

Julie Thompson (Thompson@EMBL-Heidelberg.DE)

Toby Gibson (Gibson@EMBL-Heidelberg.DE)

European Molecular Biology Laboratory

Meyerhofstrasse 1

D 69117 Heidelberg

Germany

Des Higgins (Higgins@)

EMBL outstation

The European Bioinformatics Institute

Hinxton Hall

Hinxton

Cambridge CB10 1RQ

UK

Please e-mail bug reports/complaints/suggestions (polite if possible)

to Toby Gibson or Des Higgins.

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.

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What's New (March 1996) in Version 1.6 (since version 1.5).

1) Improved handling of sequences of unequal length. Previously, we

increased the gap extension penalties for both sequences if the two sequences (or groups of previously aligned sequences) were of different lengths.

Now, we increase the gap opening and extension penalties for the shorter sequence only. This helps prevent short sequences being stretched out

along longer ones.

2) Added the "Gonnet" series of weight matrices (from Gaston Gonnet and

co-workers at the ETH in Zurich). Fixed a bug in the matrix

choice menu; now PAM matrices can be selected ok.

3) Added secondary structure/gap penalty masks. These allow you to

include, in an alignment, a position specific set of gap penalties.

You can either set a gap opening penalty at each position or specify

the secondary strcuture (if protein; alpha helix, beta strand or loop)

and have gap penalties set automatically. This, basically, is used to make gaps harder to open inside helices or strands.

These masks are only used in the "profile alignment" menu. They may be read in as part of an alignment in a special format (see the on-line help for

details) or associated with each sequence, if the sequences are in Swiss Prot format and secondary structure information is given. All of the mask parameters can be set from the profile alignment menu. Basically, the

mask is made up of a series of numbers between 1 and 9, one per position.

The gap opening penalty at a position is calculated as the starting penalty multipleied by the mask value at that site.

4) Added command line options /profile and /sequences.

These allow uses to choose between normal profile alignment where the

two profiles (pre-existing alignments specified in the files

/profile1= and /profile2=) are merged/aligned with each other (/profile)

and the case where the individual sequences in /profile2 are aligned sequentially with the alignment in /profile1 (/sequences).

5) Fixed bug in modified Myers and Miller algorithm - gap penalty score

was not always calculated properly for type 2 midpoints. This is the core alignment algorithm.

6) Only allows one output file format to be selected from command line

- ie. multiple output alignment files are not allowed.

7) Fixed 'bad calls to ckfree' error during calculation of phylip distance matrix.

8) Fixed command line options /gapopen /gapext /type=protein /negative.

9) Allowed user to change command line separator on UNIX from '/' to '-'.

This allows unix users to use the more conventinal '-' symbol

for seperating command line options. "/" can then be used in unix