* The FASTA format has been added to the list of alignment output
options.
* It is now possible to save the residue ranges (appended after the
sequence names) when saving a specified range of the alignment.
* 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"
* ClustalW now returns error codes for some common errors when exiting.
This may be useful for people who run clustalw 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)
* 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.
* Phylogenetic trees can also be saved in nexus format.
* A ClustalW icon has been designed for MAC and PC systems.
