ORFdate Parameters#

Mandatory#

• --target TARGET, -T
  Taxonomic name of the focal species.

• --mapping , -M
  CSV file matching FASTA (column 1) and tree (column 2) names.

• --tree TREE, -W
  Newick file for the phylogeny tree.

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Optional#

• -h, --help
  Show this help message and exit.

• --cpus , -P
  Total number of CPUs that can be used for the task.
  (Default: 1).

• --evalue , -E
  BLASTp e-value threshold.
  (Default: 1e-3).

• --min-coverage , -C
  Minimum query coverage threshold.
  (Default: 0.70).

• --has-underscores , -S
  Whether underscores are kept when reading the tree or considered as spaces.
  (Default: False).

• If True, underscores in species names in the tree and CSV file are treated explicitly and not replaced by spaces.

• If False, underscores in tree labels are replaced by spaces.
  Useful when the species name contains underscores (e.g., Scer_annotationV2).

• --keep-files, -K
  Keep intermediary computed files such as BLASTdb and BLAST output.

• --blast BLAST, -B
  Whether to perform BLASTp or not.
  True to perform BLASTp, False otherwise.
  (Default: True).

• --out OUT, -O
  Output directory.
  (Default: .).