CIAlign

• CIAlign
  • Summary
  • Citation
  • Mailing List
• Installation
• Usage
  • Input Files
  • Quick Start
  • Specifying Options
  • Basic Parameters
  • Cleaning Functions
    • Remove Divergent
    • Remove Insertions
    • Crop Ends
    • Remove Short
    • Remove Gap Only
    • Crop Divergent
    • Retain
  • Visualisation functions
    • Mini Alignments
    • Sequence logos
    • Statistics Plots
    • Palettes
  • Interpretation Functions
    • Consensus Sequences
    • Position Frequency, Probability and Weight Matrices
    • Similarity Matrices
  • Editing Functions
    • Extracting part of the alignment
    • Replacing U or T
    • Unaligning (removing gaps)
    • Removing Duplicates