ORFdate parameters#
Mandatory
-focal FOCAL
taxonomic name of the focal species
-names NAMES
csv file matching fasta (col1) and tree (col2) names
-tree TREE
newick file for the phylogeny tree
Optional
-h, --help
show this help message and exit
-ncpus NCPUS
total number of cpus that can be used fo the task (default: 1)
-evalue EVALUE
BLASTp evalue threshold (default: 1e-3)
-query_cov QUERY_COV
minimum query coverage threshold (default: 0.70)
-preserve_underscores
PRESERVE_UNDERSCORES (default: False). If True,
the underscores that are present in the species names in the tree and csv file are considered explicitly and not replaced by spaces. Usually underscoeres in the tree labels are replaced by spaces. Usefull when the species name contains underscores (e.g. Scer_annotationV2).