convert_to_itol

The convert_to_itol command reformats a GTDB-Tk Newick tree for visualization in iTOL: taxon labels on internal nodes are kept (with ; replaced by |), and support values are moved into square brackets after the branch lengths. To remove all internal labels instead, use remove_labels.

Arguments

usage: gtdbtk convert_to_itol --input_tree INPUT_TREE --output_tree
                              OUTPUT_TREE [--debug] [-h]

required named arguments

--input_tree

path to the unrooted tree in Newick format

--output_tree

path to output the tree

optional arguments

--debug

create intermediate files for debugging purposes

Example

Input

gtdbtk convert_to_itol --input_tree some_tree.tree --output_tree itol.tree

Output

[2022-06-30 18:44:54] INFO: GTDB-Tk v2.1.0
[2022-06-30 18:44:54] INFO: gtdbtk convert_to_itol --input_tree /tmp/decorated.tree --output_tree new.tree
[2022-06-30 18:44:54] INFO: Using GTDB-Tk reference data version r207: /gtdbtk-data
[2022-06-30 18:44:54] INFO: Convert GTDB-Tk tree to iTOL format
[2022-06-30 18:44:54] INFO: Done.