Clustal W version 1.5 now available for Mac and PC.
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 main changes over version 1.4 are:
1) ported to MAC and PC. These versions are quite slow unless you
have a nice beefy machine. On a Power Mac or a Pentium box
it is nice and fast. Two precompiled versions are supplied for Macs
(Power mac and old mac versions).
Mac: 1500 residues by 100 sequences
Power Mac 3000 " " " "
PC 1500 " " " "
2) alignment of new sequences to an alignment. Fixed a serious bug
which assigned weights to the wrong sequences. Now also, weights
sequences according to distance from the incoming sequence. The
new weights are: tree weights * similarity to incoming sequence.
The tree weights are the old weights that we derive from the tree
connecting all the sequences in the existing alignment.
3) for all platforms, output linelength = 60.
4) Bootstrap files (*.phb): the "final" node (arbitrary trichotomy
at the end of the neighbor-joining process) is labelled as
TRICHOTOMY in the bootstrap output files. This is to help
link bootstrap figures with nodes when you reroot the tree.
5) Command line /bootstrap option now more robust.
The source code is available from the EMBL file server by anonymous ftp:
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)
Thanks go to Gerhardt Vogt for generating the PC executable.
Julie Thompson and Toby Gibson (Gibson at EMBL-Heidelberg.DE)
European Molecular Biology Laboratory (EMBL)
Des Higgins (Higgins at EBI.ac.uk)
EMBL/European Bioinformatics Institute (EBI)
Cambridge CB10 1RQ