taxtastic

Taxtastic combines two pieces of functionality: extracting subsets of the NCBI taxonomy, and creating and updating reference packages of sequences for use with pplacer. All this functionality is exposed to the command line by subcommands of the script taxit. Taxtastic also supplies a clean API for dealing with reference packages. The taxonomy functionality is only available via the command line at the moment pending a complete rewrite of the taxonomy subsystem.

Contents:

• Installation
• Quickstart
  • Minimal example
  • Taxonomically equipped reference package example
• Manipulating the NCBI taxonomy
• Creating and manipulating refpkgs
  • Quickstart
  • The Refpkg format
• The Python Refpkg API
  • Accessing refpkg contents
  • Checking refpkg integrity
  • Updating and modifying refpkgs
  • Refpkg history, undo, and redo
  • pplacer specific commands
• Detailed taxit documentation
  • add_nodes
  • add_to_taxtable
  • check
  • composition
  • create
  • findcompany
  • info
  • lineage_table
  • lonelynodes
  • new_database
  • refpkg_intersection
  • reroot
  • rollback
  • rollforward
  • rp (resolve path)
  • strip
  • taxids
  • taxtable
  • update
  • update_taxids

Indices and tables

• Index

• Module Index

• Search Page