Contents

• Overview
  • Authors
  
  
• Introduction for the impatient
  • Common running modes
  • Common options to change
  • Common gripes, Cookbook and FAQ
  • Using GeneWise in a large scale throughput manner
  • Using EstWise in a large scale throughput manner
  
  
• Installation
  • Building the executables
  • Environment set up
  • Building with thread support (for SMP machines)
  • Building Perl port
  
  
• Concepts and conventions
  • Technical Approach
  • Introduction to Models in Wise2
  • Model
  • Algorithms
  • Scores
  
  
• Halfwise and Blastwise
• Principle Programs
  • genewise
  • genewisedb
  • estwise
  • estwisedb
  • Running with pthreads
  
  
• Other Programs
  • promoterwise
  • dba - Dna Block Aligner
  • psw - Protein Smith-Waterman and other comparisons
  • pswdb
  
  
• API