stackPACK^TM User Manual
Table of Contents

• Introduction
• Overview of stackPACK clustering and analysis system
• Brief instructions for use of:
• WebPipe
• WebProjectManager
• WebProbe
• WebReport
• Conventions used in stackPACK
• WebPipe clustering pipeline submission program.
• Input File Formats accepted by stackPACK.
• WebProjectManager clustering project management program
• Summary reports
• Deleting Projects
• WebProbe cluster viewer
• Querying your project by accession number
• Sequence accession number
• Cluster accession number
• Clusters and contigs with alternate expression forms
• Contig accession number
• Clonelink accession number
• Consensus accession number
• Consensus and alignment views
• Consensus View
• PHRAP Alignment View
• Final (CRAW) Alignment View
• Alignment Analysis View
• Searching for alternate expression forms
• Creating a summary report
• WebReport output generator
• APPENDIX
• Conventions used in stackPACK
• Naming conventions
• Other conventions
• Input file formats accepted by stackPACK
• Credits
• About stackPACK

• Manual for command line usage of stackPACK