infer_ranks

Establish the taxonomic ranks of the internal nodes of a rooted tree using relative evolutionary divergence (RED).

The tree is scaled with RED from the --ingroup_taxon node, using the RED of that taxon in the GTDB reference tree. Each internal node within the ingroup is then labelled with its RED value and the ranks whose median RED is within 0.1 of it, closest first, e.g. RED=0.762|family&genus. The input tree must be rooted and the ingroup taxon must be labelled in it (e.g. a tree produced by root and decorate).

Arguments

usage: gtdbtk infer_ranks --input_tree INPUT_TREE --ingroup_taxon
                          INGROUP_TAXON --output_tree OUTPUT_TREE
                          [--tmpdir TMPDIR] [--debug] [-h]

required named arguments

--input_tree

rooted input tree with labelled ingroup taxon

--ingroup_taxon

labelled ingroup taxon to use as root for establishing RED values (e.g., c__Bacilli or f__Lactobacillaceae

--output_tree

path to output the tree

optional arguments

--tmpdir

specify alternative directory for temporary files

Default: '/tmp'

--debug

create intermediate files for debugging purposes

Example

gtdbtk infer_ranks --input_tree decorated.tree --ingroup_taxon c__Bacilli --output_tree ranks.tree