Tool for visualization of chromosome tracks, synteny and genomic features
MACE is still in a pre-alpha stage and under a heavy development. The documentation has many gaps and scripts likely have many bugs or are not user-friendly yet. I highly encourage everyone to report any observed bugs, problems and suggestions by opening an issue in the MACE repository. Suggestion on new scripts and plots are very welcome too. For specific requests or collaboration (projects on Mustelidae genomics are very welcome), please email to sergei.kliver@sund.ku.dk or mahajrod@gmail.com
As of 06 April 2026, the latest version of MACE was 1.1.38.
There are two recommended ways to install MACE.
Option 1: use conda to get 'relatively stable' version of the MACE
This option makes MACE scrips available globally.
mamba install -c mahajrod routoolpa maceOption 2: install semi manually from github to get the latest version of MACE.
# Step1: install MACE and RouToolPa dependencies
mamba install 'python>=3.9' 'pandas' 'scipy' 'numpy>=1.26' 'matplotlib' 'biopython' \
'bcbio-gff' 'ete3' 'statsmodels' 'pyparsing' 'xmltodict' 'venn' 'xlsxwriter'
# Step2: clone RouToolPa and MACE repositories from github
git clone https://github.com/mahajrod/RouToolPa
git clone https://github.com/mahajrod/MACE
# Step3: add RouToolPa and MACE folders to PYTHONPATH environment variable in your ~/.bashrc file Option 2 makes MACE scripts available locally from MACE/scripts folder.
The documentation is under development, please, read help of scripts carefully. Most options have a good descriptions. In case of uncertainty or problems, open an issue in the MACE repository.
- draw_features.py - visualizes precomputed tracks in various formats on chromosomes
Figure 1: Runs of homozigosity for Martes zibelina (sable) individual 10xmzib. From Tomarovsky et al, 2026.
- draw_variant_window_densities.py - calculates and visualizes on chromosomes densities of variants from VCF file
Figure 2: Density of heterozygous SNPs for kidas (Martes zibelina x Martes martes) individual T87. From Tomarovsky et al, 2026.
- draw_coverage.py - visualizes precomputed coverage on chromosomes
Figure 3: Coverage of the Mustela nivalis (the least weasel) individual S8606. From Totikov et al, 2026.
- draw_synteny.py - visualizes pairwise synteny on chromosomes of target genome
Figure 4: Synteny plot between Mustela putorius (domestic ferret genome, target, 2n=40) and Mustela nigripes (black-footed ferret, reference, 2n=38). From Kliver et al, 2023.
- draw_macrosynteny.py - visualizes whole genome alignments
Figure 5: Macrosynteny between Mustelinae species (MNIG - NVIS) and some other Mustelidae (ELUT and MFOI). From Totikov et al, 2026.
Wiki for scripts is under development
MACE is mostly developed according to library + wrapping scripts scheme. API documentation is under development. Some library related code is still present in scripts, but eventually it will migrate.
MACE is still in a pre-alpha stage and far from being published. However, three already published articles on genomics of Mustelidae have significantly affected development of the MACE scripts. Please, cite the MACE repository (https://github.com/mahajrod/MACE) and one or several of articles from the list below, depending on what scripts have you used.
- draw_features.py or draw_variant_window_densities.py:
Tomarovsky AA, Totikov AA, Bulyonkova TM, Perelman PL, Abramov AV, Serdyukova NA, ..., and Kliver S. 2026. Genomics of Sable (Martes zibellina) × Pine Marten (Martes martes) Hybridization. Genome Biol Evol 18:evag018. https://doi.org/10.1093/gbe/evag018 - draw_macrosynteny.py:
Totikov AA, Tomarovsky AA, Perelman PL, Bulyonkova TM, Serdyukova NA, Yakupova AR, ..., and Kliver S. 2026. Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora). Genome Biol Evol 18:evag014. https://doi.org/10.1093/gbe/evag014 - draw_synteny.py:
Kliver S, Houck ML, Perelman PL, Totikov A, Tomarovsky A, Dudchenko O, ..., and Koepfli K-P. 2023. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). Journal of Heredity:esad035. https://doi.org/10.1093/jhered/esad035 - draw_coverage.py Any of above articles
Happy visualization!
Sergei Kliver