Citation
========

Protocol paper
--------------

If you use this workflow in a study, please cite the original protocol paper:

- Pacheco, M. A., Cepeda, A. S., Miller, E. A., *et al.* (2024).
  *A new long-read mitochondrial-genome protocol (PacBio HiFi) for haemosporidian parasites: a tool for population and biodiversity studies*.
  Malaria Journal 23, 134. :doi:`10.1186/s12936-024-04961-8`

Software
--------

If you publish results obtained with this codebase, consider citing the software repository
and recording the version/commit hash used for the analysis.

Suggested citation text (edit as appropriate):

.. code-block:: text

   Haemo Mito Pipeline (HmtG-PacBio-style) software, version X.Y.Z, GitHub repository: <URL>

External tools
--------------

This workflow relies on established third-party tools:

- MAFFT (multiple sequence alignment)
- BLAST+ (optional local similarity search)

Please cite these tools according to their respective publications and documentation.