README for stackPACK v2.2           	       		November 2002


This version of stackPACK replaces stackPACK v2.1.1 and includes many 
new feature requests from customers. StackPACK v2.2 contains significant 
improvements over stackPACK v2.1.1, and focuses mainly on increasing 
the accuracy of consensus sequences and improving the ability to handle 
large datasets. Enhancements made towards these goals include:

 - The incremental addition of new data to existing clusters, 
   maintaining the cluster history.
 - The inclusion of phred quality scores, contributing to accurate 
   consensus sequence generation.
 - The ability to assemble and generate consensus sequences with 
   original data, whilst still retaining the benefits of accurate 
   clustering using masked data.

Continued improvements in terms of parameterization, data management, 
viewing, and extraction functions enable more rapid assessment and 
manipulation of alignments and alignment analyses. For example, users 
can now output alignments in ACE format for improved editing in external 
programs such as consed.

Please refer to the release notes for a comprehensive summary of all 
new features and improvements in this release.


Several documentation files exist for this release:
 - README		this file
 - Release_Notes	details about the release including updates, 
                        new features and known problems
 - Install_New 		installation instructions		
 - Install_Update	instructions for updating an existing stackPACK 
                        installation

We hope that the stackPACK transcript reconstruction and variation 
analysis tools prove valuable to your research efforts and that the 
incremental addition of new data to existing clusters enhances the 
utility of stackPACK.

Your feedback is very important to us, and any comments or suggestions 
for improvement can be mailed to the stackPACK production team: 
support@egenetics.com         


Sincerely,

Liza Groenewald
Product Manager