Tools

zombi2 tools runs read-back analyses. Where the level commands simulate, the tools re-express what already exists: they read files and derive a new view of them. Each tool is a sub-subcommand — zombi2 tools <tool>. format reads a whole genomes run and writes its tables beside the run. tree and treedist work on Newick trees instead: they read one or two .nwk files and write their result to stdout by default, or to a file with -o.

format — analysis-ready tables

zombi2 tools format DIR reads a genomes run and writes tables derived from its gene trees, one --format at a time, into a directory under genomes/. It works for every resolution: family and ordered runs rebuild their gene trees from the event log; a nucleotide run recovers them from the genome, and there one table is written per declared gene — the intergenic spacer is not a gene, so it gets none. --from PATH reads a run that lives elsewhere; --flat writes the tables straight into the output directory.

Output	File	Format	Default	Contents
Homology matrix	homology_fam<f>.tsv	TSV	--format homology	one n×n table per family (n the extant leaves), in genomes/homology/. Row and column headers are the leaves n<species>\|g<copy>; each off-diagonal cell is the relation of that pair — O ortholog (their MRCA is a speciation), P paralog (a duplication), X xenolog (a transfer) — and the diagonal is -. Symmetric. A family with no surviving copy writes no table

The homology matrix is exact, not inferred. ZOMBI simulated each gene tree's embedding in the species tree, so the event at a leaf pair's most-recent common ancestor is recorded on the tree rather than reconstructed from it: a speciation there makes the pair orthologs, a duplication paralogs, a transfer xenologs. That is what makes these tables a ground-truth reference to score an orthology-inference method against.

tree — one transform on a Newick tree

zombi2 tools tree TREE applies a single transform to a Newick tree and writes the result — Newick to stdout, or to a file with -o. Exactly one action runs per call. TREE is a tree file, or - to read the tree from stdin.

The actions split by whether they need each tip's fate. --prune does: it drops the dead and unsampled lineages to leave the extant tree, so it reads the fates a ZOMBI complete tree carries (an ultrametric tree, whose tips are all contemporaneous, counts as all-extant). A plain non-ultrametric tree with no fates is refused. The rest — the geometric transforms and --red — ignore fates and load any tree, so an inferred phylogram or a rounding-noisy dated tree goes through them unchanged.

Action	What it writes
--prune	the extant tree: the dead and unsampled lineages dropped, and the unifurcations they leave behind suppressed so the tree stays bifurcating
--round	the tree snapped to exactly ultrametric, by extending the terminal branches to a common depth. --tol is the tolerance as a fraction of tree height (default 1e-3); a tip-depth spread wider than that raises, because it is real tip-date signal — extinct lineages or serial samples — not rounding
--stem LEN / --stem-add LEN	the branch above the crown set to LEN, or extended by LEN; nothing below the crown moves
--rescale-height H / --rescale-factor F	every branch length scaled — so the root-to-tip height becomes H, or by a raw multiplier F
--red	the RED-rescaled tree: node depths become their Relative Evolutionary Divergence (Parks et al. 2018), ultrametric on [0, 1] with the root at 0 and every tip at 1. --red --values writes a two-column node<TAB>RED table instead of a tree

# drop the extinct lineages, extant tree to stdout
zombi2 tools tree out/species/species_complete.nwk --prune

# snap a rounding-noisy dated tree to ultrametric, to a file
zombi2 tools tree dated.nwk --round -o dated_ultrametric.nwk

# the RED of every node, as a table
zombi2 tools tree out/species/species_extant.nwk --red --values

treedist — distance between two trees

zombi2 tools treedist TREE_A TREE_B reports how far apart two rooted trees are over their shared tips, printed as <metric><TAB><value> to stdout (or a file with -o). Pick the metric with --metric:

--metric	Distance
rf (default)	Robinson–Foulds — the number of clades present in one tree but not the other
rf-normalized	that count over the total number of non-trivial clades, so it lands in [0, 1]
branch-score	Kuhner–Felsenstein — the square root of the summed squared branch-length differences over every clade, terminal branches included; unlike RF it moves even when only the branch lengths differ
all	every metric above, one per line

The tips are matched by label — the tip name for an external tree, or n<id> for a ZOMBI tree — so a true tree and an inferred tree line up by taxon, whatever order their files list the tips in. The two trees must carry the same tip set: a differing leaf set is an error, not a partial score.

# Robinson–Foulds between a true tree and an inferred one over the same tips
zombi2 tools treedist true.nwk inferred.nwk --metric rf

# every metric at once
zombi2 tools treedist true.nwk inferred.nwk --metric all

The rest

The remaining scoring and reconciliation commands (reconciliation-accuracy, the undated simulator, the ALE likelihood) are quarantined during the clean-core rebuild; their files are documented here as each returns.