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Introduction to Version D 2.0

This is the first major update to the AMPS package since its initial distribution in 1988 (Version D 1.0). No major changes have been made to the basic multiple alignment functions, except the addition of a dendrogram drawing facility in programme ORDER and the provision of identifier codes of up to 20 characters (including the '>' symbol) (program PATT is limited to 10 characters). Existing users should not experience problems - I hope... The major addition is the availability of the flexible pattern matching and database scanning features of the programmes described in Barton, 1990 and Barton &Sternberg 1990. Sections have been added to this guide to explain how these features may be used.

All development of this package is now carried out on a Sun Microsystems SPARCstation under the Unix operating system. The most stable version is therefore the SPARCstation one. With this release is the first option for Silicon Graphics Personal Iris and compatibles. The core multiple alignment programs will compile under VAX/VMS - see the instructions in BUILD.COM.

If you have problems with the programs and your local Guru cannot solve them, then e-mail me on stating exactly what the problem is, together with example files.