gtdb-itol-decorate

Creates iTOL files for tree decoration, given a set of GTDB genomes.

Installation

pip install gtdb-itol-decorate

Usage

This program requires a taxonomy file (available from the GTDB website), e.g. bac120_taxonomy.tsv, or ar53_taxonomy.tsv.

gtdb_itol_decorate /path/to/tree.tree /path/to/taxonomy.tsv /path/to/output

Output

The program will output the following files.

Note: Typical use will be:

1. Upload [name_of_input_tree].tree_stripped
2. Drag the following files into the tree: itol_dataset_strip_phylum.txt, itol_labels.txt, itol_popup.txt, itol_tree_colours.txt
3. Use the itol_collapse_[rank].txt files to manipulate the view of the tree as desired.

[name_of_input_tree].tree_stripped

This is the tree that you should upload to iTOL. It has been stripped of all internal labels to match the iTOL tree format.

itol_collapse_[rank].txt

When this file is dropped into the iTOL tree, it will collapse all nodes at this rank.

itol_dataset_strip_phylum.txt

This file will create a new colour strip for each phylum.

itol_labels.txt

This will add taxon labels to the tree for both the internal and leaf nodes.

Note: To enable internal labels:

• Open the "Control panel"
• Select the "Advanced" tab.
• Under "Branch metadata display", make sure "Node IDs" is set to "Display".

itol_popup.txt

This creates a popup window when the mouse is hovered over each leaf node. It will display the genome id, and full taxonomy string.

itol_tree_colours.txt

Creates a colour range for each taxon, based on the phylum colour. It will increase in brightness from phylum to species.

Note: This can be changed by altering the "Coloured ranges" popup that will appear after adding this file. In the "Cover" option, "Clade" view is recommended.