FastSubtrees

• Fastsubtrees
  • Introduction
  • Working with the library
    • Installation
    • Command line interface
      • CLI example: working with the NCBI taxonomy tree
      • Using NtSubtree
    • API
      • API example: working with the NCBI taxonomy tree
      • Using NtSubtree
    • Docker
    • Tests
    • Benchmarks
    • Example application: Genome attributes viewer
      • Local installation and startup
    • Other subpackages
      • NtSubtree
      • ntdownload
      • ntmirror
    • Internals
      • Tree construction algorithm
      • Parallelizing the tree construction
  • Community guidelines
  • Documentation
  • Licence
  • Acknowledgements
• Command line interface
  • Tree construction
    • Construction from a tabular file
    • Generalized tree construction
  • Modifying an existing tree representation
    • Updating or resetting a tree
    • Adding leaf nodes or new subtrees
    • Removing leaf nodes or subtrees
    • Attributes when editing a tree
  • Tree attributes
    • Adding an attribute
      • Attribute values from a tabular file
      • Generalized source of attribute values
    • Listing defined attributes
    • Editing attribute values
  • Subtree queries
• Library API
  • Construction of the tree representation
    • Constructing from a tabular file
    • Constructing from a different data source
  • Saving to and loading from file
  • Modifying an existing tree representation
    • Adding nodes
    • Removing nodes
    • Moving a node
    • Updating or resetting a tree
  • Working with attributes
    • Creating attributes
    • Modifying attributes
    • Checking if an attribute exists
    • Destroying attributes
  • Subtree queries
    • List of IDs of a subtree
    • Attribute values in a subtree
  • Verbosity
• NtSubtree
  • Installation
  • CLI
    • Example usage
  • API
    • Example usage
• Genomes Attributes Viewer
  • Installation
  • Starting the application
  • Usage
• NtDownload
  • Installation
  • Command line interface
    • ntdownload
    • ntnames
  • API
    • Downloader
    • Scientific names iterator
  • Test suite
• NtMirror
  • Requirements
  • CLI
    • Loading into the database
    • Subtree search using hierarchical SQL
    • Example usage
  • API
    • Database setup
    • Loading the data using MariaDB
    • Example usage
    • Loading the data using another RDBMS
  • Tests