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Run integrated pipelines.

Input:

  • pl is a command group; use one of its subcommands directly.

Notes:

  • Currently implemented subcommand:
    • condense: condense monophyletic subtrees based on a taxonomy TSV file.
  • Run necom pl <subcommand> --help for command-specific options.
  • Reads from stdin if input file is ‘stdin’.

Examples:

  1. Show available subcommands necom pl --help