Tree rendering

What they are

We provide pre-formatted tree with metadata files which can be directly parsed and rendered by FigTree and iTOL.

How to display them

FigTree

Simply open figtree.tre in FigTree.

  • This file is a pre-decorated FigTree Nexus file. It comes with tip and internal node labels (taxonomy and branch supports) and a default collapsing scheme. The “colored” version also has branch colors.

iTOL

  • Upload pruned_tree.nwk and open in the iTOL interface.
    • If iTOL prompts to auto-collapse, click “Reset all”.
  • Sequentially drag & drop the following files into the iTOL interface. Ignore errors (they are the unused labels). Save changes.
    • collapse.txt: Colllapsing scheme.
    • label.txt: Node labels, including both tips (genomes) and internal nodes (they now become tips after collapsing).
  • (The following are optional “datasets” for iTOL.)
    • branch_text.txt - Labels to be shown on branches.
    • xxx_node_text.txt - Branch support values as node labels (“xxx” is the type of branch support).
    • xxx_branch_color.txt - Branch support values as branch color gradient.
  • (The following are only for astral.e5p50, which has a pre-defined coloring scheme.)
    • branch_color.txt
    • clade_color.txt
    • label_color.txt

Moreover

The file collapsed_tree.nwk is a shrinked Newick file with tips representing collapsed clades.

How they were generated

The workflow starts with a tree and taxonomic annotation (NCBI or GTDB, pre-curated using tax2tree).

It collapses the tree at given rank(s). One can specify multiple ranks and complex criteria for inclusion at each rank. In the current data release, the default criteria are:

  • Sequentially collapse at the following ranks:

    • genus => family => order with 50 or more taxa => class with 5 or more taxa => phylum with at least one taxon => taxonomic units above phylum (if available).

  • If a lower-rank clade is already collapsed, its higher-rank ancestors will not be collapsed.

  • If a taxonomic unit is polyphyletic, minor clades which have less than 5% taxa of the primary clade will be deleted.

    • e.g., say Firmicutes_1 has 1,000 tips. If Firmicutes_10 has 45 tips (< 1000 * 5%), it will be deleted.

  • Tips that do not belong to any collapsed clades will be deleted.

For a special set of 1k-taxon trees, more relaxed parameters were used:

  • genus => family with 10 or more taxa => order with 5 or more taxa => class => phylum with at least one taxon

It adds taxonomic labels to branches / nodes. They are the taxonomic units that exclusively describe the corresponding branches. If multiple ranks can describe one branch, only the highest-rank is retained.

Optionally, one can provide additional node metrics (e.g., branch support values), which will be converted into node labels and color gradients.

How I can generate them

We provided the source code for generating the pre-formatted tree files.