Welcome to AACon’s documentation!

AACon’s documentation is also available in pdf. Download it here!

Contents:

• Getting Started
  • Benefits
  • Distributions
    • Jalview and JABAWS
    • Standalone Client
    • Web service
• Included Methods
  • Valdar
  • SMERFS
  • References
• Standalone Client
  • Executing AACon
  • Input
  • Output
  • Calculating conservation
  • Custom gap character
  • Running SMERFS with custom parameters
  • Outputing to a file
  • Execution details
  • Results normalization
  • Conservation for large alignments
• Web Service
  • Web Service Details
  • Using Web Service CLI Client
  • Structure of the command line client
  • AACon web service functions overview
  • Building web services artifacts
  • Connecting to AAConWS
  • Calculating conservation
  • Checking the status of the calculation
  • Calculating conservation with presets
  • Calculating conservation with custom parameters
  • A complete AAConWS web service client example
• Java Library
  • Using the library
  • Loading data
  • Initialising the executor
  • Normalisation
  • Setting the conservation methods
  • Output the results
  • Example
• Citations
• Changelog
  • Version 1.1 (Released 19 May 2017)
  • Version 1.0 (Released 16th Dec 2011)

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Note

This is an open source project. If you want to contribute or report an issue have a look at our Github repository.