@deckyard/mitoleaf

Reads the mitoLEAF human mitochondrial phylogeny (the maintained successor to PhyloTree), turns a haplogroup into its defining haplotype with back mutations applied, and finds the haplogroup nearest an observed haplotype. Haplotypes are lineage.MtHaplotype values from @deckyard/forensicgenetics. Pure Jennifer, TinyGo-clean.

Manual: https://deckyard.github.io/deck-mitoleaf/

Install

Requires Jennifer 0.25.0 or newer.

jvc add "@deckyard/mitoleaf" "^0.1.0"
jvc install

jvc vendors the deck to vendor/deckyard/mitoleaf/ and pulls in @deckyard/forensicgenetics with it. Without jvc, copy the src/ of both decks (from a checkout or a deckyard-mitoleaf-<version>.tar.gz release archive) by hand:

mkdir -p vendor/deckyard/mitoleaf vendor/deckyard/forensicgenetics
cp path/to/deck-mitoleaf/src/*.j         vendor/deckyard/mitoleaf/
cp path/to/deck-forensicgenetics/src/*.j vendor/deckyard/forensicgenetics/
rm -f vendor/deckyard/*/*_test.j

Example

No tree is bundled; download the phm XML from mitoLEAF.

import "@deckyard/mitoleaf/" as mitoleaf;
import "@deckyard/forensicgenetics/lineage.j" as lineage;

def t as mitoleaf.Tree init mitoleaf.parse(fs.readString("mitoLEAF_phm.xml"));

mitoleaf.path($t, "L0a1");                               # root first
mitoleaf.motif($t, "L0a1");                              # this node's own tokens
lineage.mtDesignations(mitoleaf.haplotype($t, "L0a1"));  # accumulated haplotype

def m as mitoleaf.Match init mitoleaf.assign($t, $observed);

assign is a nearest-neighbour report, not a haplogroup classifier; see Limitations.

Tests

From the deck root (the example reads testdata/tree.xml):

jennifer test src/mitoleaf_test.j
jennifer run examples/haplogroups.j

Citing mitoLEAF

Huber N, Hurmer N, Dür A, Parson W. mitoLEAF: mitochondrial DNA Lineage, Evolution, Annotation Framework. NAR Genomics and Bioinformatics 7(2), 2025. https://doi.org/10.1093/nargab/lqaf079

mitoLEAF data is MPL-2.0; none is redistributed here.

Licence

LGPL-3.0-only, see LICENSE. Copyright (C) 2026 mplx <mplx@jennifer-lang.dev>.