These are the mitogenome related sources including MITOS and other (more or less) helpful tools. Note that some of the tools are unfinished and not in a production state.

Usage on Galaxy

MITOS should primarily be used via Galaxy. It is available for instance on usegalaxy.eu

MITOS2
MITOS

Installation

There are two ways to install. Preferred is the installation via conda since this also takes care of non-python requirements of the main mitos script.

via conda: conda create --strict-channel-priority -c conda-forge -c bioconda -n mitos2 "mitos>=2"
- this will create a conda environment and install MITOS2. For MITOS use conda create --strict-channel-priority -c conda-forge -c bioconda -n mitos "mitos<2"
- enable the conda environment with conda activate mitos2 (resp. conda activate mitos)
- in case of problems with resolving environments try to use use --solver libmamba or replace conda by mamba.
via pip: pip install mitos

For the non-python requirements see README.MITOS.

Development Setup

For developers who want to contribute to MITOS:

Fork the repository on GitLab: https://gitlab.com/Bernt/MITOS

Clone your fork:

git clone https://gitlab.com/YOUR_USERNAME/MITOS.git
cd MITOS

Set up development environment:

Option A: Python-only (for basic development):

pip install -r dev_requirements.txt

Option B: Full conda environment (required for integration tests):

# Create conda environment with all dependencies
conda create --strict-channel-priority -c conda-forge -c bioconda -n mitos-dev python=3.7 \
  biopython=1.73 blast>=2.9 hmmer=3.4 infernal>=1.1.5 viennarna r-base r-ggplot2 \
  r-reshape2 openjdk reportlab pillow libtiff pip

# Activate environment and install MITOS in development mode
conda activate mitos-dev
pip install -r dev_requirements.txt

Optional: Set up pre-commit hooks for automatic linting:
```
pip install pre-commit
pre-commit install
```
This will automatically take care of things like trailing whitespace, empty lines at the end of files and it will run black, isort, flake8 and mypy before each commit. See configuration in .pre-commit-config.yaml.

Development Workflow

Running tests:

# Linting and code style
tox -e lint

# Type checking
tox -e type

# Unit tests
tox -e py37

# Integration tests (requires conda and reference data)
tox -e integration-py37

Before submitting a merge request:

Ensure all tests pass: tox
Follow the existing code style
Add tests for new functionality
Update documentation if needed

MITOS

runmitos.py: standalone CLI MITOS

From runmitos.py help:

mandatory options:
  -c CODE, --code CODE  the genetic code
  -o OUTDIR, --outdir OUTDIR
                        the directory where the output is written
  --linear              treat sequence as linear (not mandatory for circular sequences)
  -r REFSEQVER, --refseqver REFSEQVER
                        directory containing the reference data (relative to --refdir)

Please note that the reference data for the -r flag needs to be downloaded from Zenodo (MITOS, MITOS2).

see also runmitos.py --help or README.MITOS

genbank file handling

refseqsplit:
- splits a file consisting of concatenated gb files into single genbank files
- its possible to apply filters (taxonomy, prefix)

skewness related programs

skew: compute skewness values for a gene of given genbank files
skewcum: compute cumulative skewness for given genbank files
skewsvm: do svm classification of skewness values .. and try to relate misclassifications to rearrangements

MISC

gcpp
- pretty print and compare genetic code

Environment
- Console
Intended Audience
- Science/Research
Operating System
- OS Independent
Programming Language
- Python :: 3
Topic
- Scientific/Engineering :: Bio-Informatics

Metadata

Environment
- Console
Intended Audience
- Science/Research
Operating System
- OS Independent
Programming Language
- Python :: 3
Topic
- Scientific/Engineering :: Bio-Informatics

Release files for mitos 2.1.10

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mitos 2.1.10
File	Size	Uploaded
mitos-2.1.10.tar.gz	542.9 kB	Dec 8, 2025	Details

Built distribution (wheel)

Table of built distributions (wheels) for mitos 2.1.10
File	Interpreter	ABI	Platform	Reset
mitos-2.1.10-py3-none-any.whl 602.3 kB Dec 8, 2025	Python 3	none	any	Details

Total release size: 1.1 MB

Release files / mitos-2.1.10.tar.gz

Download URL	mitos-2.1.10.tar.gz
Size	542.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`0fcc84806fcca5a5dc49b5acd3874c499e72349a5648bb58a9d4870604a36c21`
BLAKE2b-256 checksum How to use checksums	`4ce842c2f90c5b39169b7535c7234fd17cbf88ebc951076ce7c9e9bc21f40650`
Upload date	Dec 8, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.7.17`

Release files / mitos-2.1.10-py3-none-any.whl

Download URL	mitos-2.1.10-py3-none-any.whl
Size	602.3 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`07645d3f1a7629b236bacc06321fb2ac4335e33bc1ce176e7c1107c1f525b505`
BLAKE2b-256 checksum How to use checksums	`ac1df799f5dc7e3159c8892935e062953ae7d684a79dea577012a3de2380c8a9`
Upload date	Dec 8, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.7.17`