# name-tree

Translate a numerically-labelled tree export (TNT, PhyG, or any plain Newick file with bare `1`, `2`, `3`, … leaf labels) back to real taxon names, reading the label order from the FASTA that produced it.

```bash
obikmer name-tree TREE --fasta FASTA -o OUTPUT
```

## Arguments

| Argument | Description |
|---|---|
| `TREE` | Tree file to translate — a TNT-style NEXUS export (`tree NAME = [&U] ...;`) or a plain Newick file |
| `--fasta` | FASTA file whose record order gives the numeric taxon labels (1-based) — typically the `_sankoff.fasta`/`_snp.fasta` used to produce `TREE` |
| `-o, --output` | Output NEXUS file path |

## Output

A NEXUS file with a `taxa` block, a `translate` table (numeric label → taxon name, from `--fasta`'s header order), and every tree found in `TREE`, topology unchanged — readable directly in FigTree, PearTree, `ape` (R), etc.

`--tnt`'s and `--phyg`'s exports (see [phylo](phylo.md)) both number taxa `1..N` in the same order as the pseudo-alignment FASTA they were built from (`<prefix>_sankoff.fasta`), so pass that same file as `--fasta` here.