MiTo (Mitochondrial single-cell lineage tracing Toolkit)
Mitochondrial single-cell multi-omics in Python.
MiTo infer clonal ancestries in single-cell data from natural mtDNA variation.
The framework provides the infrastructure to convert MAESTER, scmtATAC-seq and RedeeM pre-processing outputs into Allele Frequency Matrices (i.e., AnnData objects), filter informative mtDNA variants, genotype individual cells, and infer mitochondrial phylogenies and clones for dowstream multi-omic analysis.
Installation
pip install scmito
Requires Python 3.11+.
import mito as mt
print(mt.__version__)
Quick start
import scanpy as sc
import mito as mt
# Allele Frequency Matrix (cell x site AnnData with AD / DP layers)
afm = sc.read('afm_unfiltered.h5ad')
# Cell and variant filters, distances in mtDNA mutation space
afm = mt.pp.filter_cells(afm, cell_filter='filter2')
afm = mt.pp.filter_afm(afm, filtering='MiTo')
# Phylogeny and clonal inference
tree = mt.tl.build_tree(afm, precomputed=True, solver='UPMGA')
annotator = mt.tl.MiToTreeAnnotator(tree)
annotator.clonal_inference()
# Visualization
mt.pl.plot_tree(tree, features=['MiTo clone'])
See getting-started tutorial for the full vignette.
API
MiTo follows the scverse layout, composing with scanpy and anndata:
| Module | Purpose |
|---|---|
io |
Build AFMs from pre-processing outputs, read/write Newick tree objects |
pp |
Cell and variant filtering, genotying, distances, kNN graphs, embeddings |
tl |
Tree building, clonal inference, clustering, fate bias |
pl |
Trees, heatmaps, embeddings, coverage and variant-spectrum plots |
ut |
Metrics, helpers |
Supported platforms: scRNA-seq (MAESTER), scmtATAC-seq and 10x MultiOme (RedeeM).
Full reference: MiTo docs.
Development
git clone https://github.com/andrecossa5/MiTo.git
cd MiTo
pip install -e ".[test]"
pytest
Citation
If MiTo is useful in your work, please cite:
Cossa, A. Dalmasso A. et al. MiTo: mitochondrial lineage tracing and single-cell multi-omics. Nat Comm (2026). https://doi.org/10.1038/s41467-026-71607-5
MiTo builds on the Cassiopeia package for phylogeny reconstruction and data infrastructure. Please, cite it as well.
Releases
See CHANGELOG.md.
License
MIT — see LICENSE.
1 maintainer
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