Introduction to needle tools

BMERC : Index of needle software : needle tools : Introduction

These pages contain introductory and overview material, including examples.

• General information about needle tools
  • What is needle tools?
  • Credits and acknowledgements
  • Documentation conventions
  • Using needle tools
• Overview of the prediction process
  • Prediction steps
  • Generating the core library
  • Generating multiple homolog alignments
  • Generating MRF files
  • Running needle
• Introduction to MRF score generation
  • Outline of MRF generation programs and files
  • GMT marginal sets
  • MRF implementation details
    • Environment encoding
• Dependency files for make
  • About make and dependency files
    • makefile syntax
    • Macros used to invoke commands
    • How make works
  • Dependency file generator arguments
    • Standard arguments to dependency file generators
    • File-type-specific arguments
    • Defined file types
    • The -search-path feature
    • Only one generator per directory
    • The -use-plus feature
  • Which files are constructed
    • Exceptional cases
  • Targets and macros
  • MRF-specific dependency generator arguments
    • Cross-validation
    • Sharing cross-validation set score files
• Core library construction examples
  • Sample script
  • Automatic generation of cores via makefiles
    • The core list file
    • The makefile
    • Making the dependency file
    • Making the core and sequence files
    • Testing the core generation results
• MRF generation examples
  • Sample script
    • Customization of directories
    • make-mrf-files arguments
    • Environments and counts
    • Compute total counts
    • Compute score files
  • Automatic generation via makefiles
    • Generating a complete set of score/env files
      • The cross-validation set file
      • The marginal definition file
      • The makefile
      • Making the dependency file
      • Making the score and environment files
    • Generating "add-on" score/env files
• Threading alignment experiments
  • Running threading alignment experiments
  • Grading threading alignment results
    • Grading cross-threadings using ctimaps
    • Grading cross-threadings using alignments