rsomics-tree-tipdist 0.1.0

Patristic tip-to-tip distance matrix from a phylogenetic tree (sum of branch lengths between every pair of tips) — scikit-bio TreeNode.cophenet equivalent, byte-exact TSV
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# rsomics-tree-tipdist

Patristic tip-to-tip distance matrix from a phylogenetic tree: for every pair
of tips, the sum of branch lengths along the path connecting them. Output is a
square, labelled, symmetric distance matrix in scikit-bio `DistanceMatrix`
(lsmat) TSV form, byte-identical to skbio.

```
rsomics-tree-tipdist tree.nwk -o dm.tsv
cat tree.nwk | rsomics-tree-tipdist --count        # count branches, not lengths
```

Tip labels are emitted in postorder tip order, exactly as skbio's
`TreeNode.cophenet`. Missing branch lengths are treated as 0. This is the
natural input producer for `rsomics-pcoa` / `rsomics-permanova`.

This is the *phylogenetic* cophenetic (patristic) distance. It is distinct from
`rsomics-cophenet`, which computes the scipy linkage-matrix cophenetic distance
of a hierarchical clustering — different algorithm, different input.

## Origin

This crate is an independent Rust reimplementation of scikit-bio's
`skbio.tree.TreeNode.cophenet` / `TreeNode.tip_tip_distances` (skbio 0.7.2),
based on:

- The published patristic-distance method: Fourment, M., & Gibbs, M. J. (2006).
  PATRISTIC: a program for calculating patristic distances. *BMC Evolutionary
  Biology*, 6, 1. https://doi.org/10.1186/1471-2148-6-1
- The scikit-bio BSD-3-Clause source (`skbio/tree/_tree.py`,
  `skbio/io/format/lsmat.py`), which is permissively licensed and may be read
  and cited. The accumulation order and the lsmat TSV float formatting (CPython
  `repr` shortest round-trip) were matched against it for byte-exact output.

Test fixtures are independently generated and verified against the upstream
binary.

License: MIT OR Apache-2.0.
Upstream credit: scikit-bio https://scikit-bio.org (BSD-3-Clause).