Clustal W version 1.6 now available. March 1996.
Clustal W is a complete overhaul and upgrade of the Clustal V multiple
sequence alignment program. It 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.
The source code is available from the EMBL file server by anonymous ftp:
ftp.ebi.ac.uk
unix pub/software/unix/clustalw.tar.Z (compressed tar archive)
vms pub/software/vms/clustalw.uue (uuencoded ZIP archive)
mac pub/software/mac/clustalw.sea.hqx (self extracting archive/binhex)
PC pub/software/dos/clustal$.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.
The main changes over version 1.5 are:
1) Improved handling of sequences of unequal length. 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 protein secondary structure/gap penalty masks.
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.
4) Added new command line options for dealing with profiles and masks:
***Profile Alignments:***
/PROFILE :Merge two alignments by profile alignment
/SEQUENCES :Sequentially add profile2 sequences to profile1 alignment
***Structure Alignments:***
/NOSECSTR1 :do not use secondary structure/gap penalty mask for profile 1
/NOSECSTR2 :do not use secondary structure/gap penalty mask for profile 2
/SECSTROUT= :STRUCTURE or MASK or BOTH or NONE output in alignment file
/HELIXGAP=n :gap penalty for helix core residues
/STRANDGAP=n :gap penalty for strand core residues
/LOOPGAP=n :gap penalty for loop regions
/TERMINALGAP=n :gap penalty for structure termini
/HELIXENDIN=n :number of residues inside helix to be treated as terminal
/HELIXENDOUT=n :number of residues outside helix to be treated as terminal
/STRANDENDIN=n :number of residues inside strand to be treated as terminal
/STRANDENDOUT=n:number of residues outside strand to be treated as terminal
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 '-'.
Julie Thompson and Toby Gibson (Gibson at EMBL-Heidelberg.DE)
European Molecular Biology Laboratory (EMBL)
Meyerhofstrasse 1
69117 Heidelberg
Germany
Des Higgins (Higgins at EBI.ac.uk)
EMBL outstation
The European Bioinformatics Institute (EBI)
Hinxton Hall
Hinxton
Cambridge CB10 1RQ
UK.
