[Neclow]

Summary

Adds a Core concepts notebook between Getting started and Tree operations, explaining what a Phylo2Vec vector encodes. Related to #170; follows up on #222.

The text and figures are adapted from the background and methods of Neil Scheidwasser's PhD thesis and the Phylo2Vec papers. Each claim is checked by a code cell against the current code (e.g., the 105 vectors with 5 leaves map to 105 distinct trees, and each step of the vector → tree figure matches to_newick).

Contents

1. Phylogenetic trees: definitions and the size of tree space, (2n-3)!!
2. Why a vector?: Newick strings are not one-to-one, vectors are
3. The Phylo2Vec vector: node and branch labels, the definition v[j] ∈ {0, ..., 2j}, ordered and unordered vectors
4. Other tree formats: edges, ancestry and pairs (moved from Getting started)
5. From a vector to a tree: leaf-by-leaf construction, internal node relabelling, pairs
6. From a Newick string to a vector: parsing, ancestry sorting (with and without parent labels), vector building with a Fenwick tree
7. Branch lengths: the matrix format
8. Complexity of the conversions

Figures

The thesis TikZ figures are added as SVGs in docs/notebooks/img/, with a white background so that they render in dark themes. One fix compared to the thesis: the last row of the relabelling figure now reads "Label the parent of 3 as 8" (it said 1).

Other changes

• Getting started: the "Other tree formats" section moved to Core concepts; remaining sections renumbered, with links to Core concepts
• Tree operations and Statistics link to Core concepts
• _toc.yml and the CI notebook job include the new notebook