tog

The tog command makes a tree with every placed query added as a pendant edge at its best placement, as guppy tog (pplacer v1.1.alpha19) does, so that no pplacer installation is needed. The output is the same file, byte for byte: Newick (.tog.tre), or phyloXML with --xml (.tog.xml), with guppy’s options and output names (-o, --out-dir, --prefix, one tree per placefile, placefile:groups.csv to split one jplace into one tree per group).

What guppy does, and so what tog does:

  • A query becomes a leaf named after it (branch length = its pendant length), attached at its distal length on the edge of its best placement; a query written as one record with several names becomes a node with one zero-length leaf per name.

  • The best placement is the one with the highest like-weight ratio (the first in pplacer’s order), also with --pp: in pplacer’s code the comparison never looks past the first placement, so --pp only requires posterior probabilities to be present.

  • --node-numbers writes the reference tree’s node numbers where bootstraps go ([n]) and prefixes its labels with @.

Arguments

usage: gplace tog [-o FILE] [--out-dir DIR] [--prefix PREFIX] [--pp] [--xml]
                  [--node-numbers] [-h]
                  placefile [placefile ...]

Positional Arguments

placefile

jplace file(s)

guppy tog options

-o

Specify the filename to write to.

--out-dir, --out_dir

Specify the directory to write files to.

--prefix

Specify a string to be prepended to filenames.

--pp

Use posterior probability for the weight.

--xml

Write phyloXML (with colors) for all visualizations.

--node-numbers, --node_numbers

Put the node numbers in where the bootstraps usually go.

Example

gplace tog -o gtdbtk.bac120.classify.tree pplacer.bac120.json      # as GTDB-Tk runs guppy tog
gplace tog --xml --out-dir trees/ placements_*.jplace

Validation

Compared with the stock guppy on 607 cases, every output file identical: GTDB-Tk’s 112 class-level jplaces and gPlace’s test jplaces with each option set, a 4,040-query jplace on the full GTDB bacterial tree, every combination of -o / --out-dir / --prefix, several placefiles, gzipped input, placefile:groups.csv splitting, and synthetic placements (labels that need quoting or XML escaping, ties, placements at the ends of an edge, multi-name records, float-like labels, posterior probabilities).