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Command reference

tact_build_taxonomic_tree

Generates a taxonomic tree from TAXONOMY.

TAXONOMY is a comma-separated values file with several requirements:

  • Each row represents a single species.
  • Each column represents a taxonomic rank.
  • The columns must be arranged from most inclusive to least inclusive, with the last column as the species name.
    • e.g. Family,Genus,Species
  • Each rank must be named
  • Each rank must be unique
    • OK: Cichlidae,Cichla,Cichla temensis
    • NO: Cichlidae,Cichlidae,Cichla temensis
    • NO: Cichlidae,,Cichla temensis

See the taxonomy CSV file in the examples/ folder for a working example.

tact_add_taxa

Adds unsampled taxa from a complete taxonomic phylogeny (generated from tact_build_taxonomic_tree) onto a backbone phylogeny.

tact_check_results

Checks the result of the output from tact_add_taxa.


Last update: October 11, 2021