ESZlab1

EZmito Web Server

powered by ESZ_lab (University of Siena)

EZmito2 is a bioinformatic toolkit for phylogenetic data preparation, nucleotide composition analysis of mitogenomes, detection of chimeric regions produced during the assembly process and other functions.

(version 2026.3, March 2026)

Citations

If you use EZmito2 for a scientific publication, please cite:

  • Cucini, C., Pons, J., Funari, R., Carapelli, A., Frati, F., & Nardi, F. (2026). EZmito2: a tool suite for mitochondrial genome dataset preparation, population genetics, and visualization. Molecular Biology and Evolution, 43(8), msag210. Doi: 10.1093/molbev/msag210

If you used EZcircular, please also cite:

  • Dale, R. K., Pedersen, B. S., & Quinlan, A. R. (2011). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24), 3423–3424. Doi: 10.1093/bioinformatics/btr539
  • Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422. Doi: 10.1093/bioinformatics/btp163

If you used EZcodon, please also cite:

  • Lee, B. D. (2018). Python implementation of codon adaptation index. Journal of Open Source Software, 3(30), 905. Doi: 10.21105/joss.00905
  • Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. Doi: 10.1109/MCSE.2007.55
  • Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422. Doi: 10.1093/bioinformatics/btp163
  • McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51–56. Doi: 10.25080/Majora-92bf1922-00a

If you used EZdist, please also cite:

  • Harris, C. R., Millman, K. J., Van Der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., et al. (2020). Array programming with NumPy. Nature, 585(7825), 357–362.
  • McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51–56. Doi: 10.25080/Majora-92bf1922-00a
  • Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. Doi: 10.1109/MCSE.2007.55
  • Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., et al. (2020). SciPy 1.0: fundamental algorithms for scientific computing in Python. Nature Methods, 17(3), 261–272. Doi: 10.1038/s41592-019-0686-2

If you used EZmix, please also cite:

  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10(1), 421. Doi: 10.1186/1471-2105-10-421
  • Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. Doi: 10.1109/MCSE.2007.55
  • McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51–56. Doi: 10.25080/Majora-92bf1922-00a

If you used EZpipe, please also cite:

  • Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. Doi: 10.1093/molbev/mst010
  • Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17(4), 540–552. Doi: 10.1093/oxfordjournals.molbev.a026334
  • Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422. Doi: 10.1093/bioinformatics/btp163

If you used EZpopstat, please also cite:

  • Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2), 479–491. Doi: 10.1093/genetics/131.2.479
  • Harris, C. R., Millman, K. J., Van Der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., et al. (2020). Array programming with NumPy. Nature, 585(7825), 357–362.
  • McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51–56. Doi: 10.25080/Majora-92bf1922-00a

If you used EZpcoA, please also cite:

  • Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2), 111–120. Doi: 10.1007/bf01731581
  • Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. Doi: 10.1109/MCSE.2007.55
  • McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51–56. Doi: 10.25080/Majora-92bf1922-00a

If you used EZskew, please also cite:

  • Hassanin, A., Leger, N. E. L. L. Y., & Deutsch, J. (2005). Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Systematic Biology, 54(2), 277–298. Doi: 10.1080/10635150590947843
  • Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95. Doi: 10.1109/MCSE.2007.55
  • Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422. Doi: 10.1093/bioinformatics/btp163
  • McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51–56. Doi: 10.25080/Majora-92bf1922-00a

If you used EZsplit, please also cite:

  • Dale, R. K., Pedersen, B. S., & Quinlan, A. R. (2011). Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics, 27(24), 3423–3424. Doi: 10.1093/bioinformatics/btr539

If you used EZtrampo, please also cite:

  • Cucini, C., Nardi, F., & Pons, J. (2026). Integrating Secondary Structure Information Enhances Phylogenetic Signal in Mitochondrial Protein Coding Genes. Systematic Biology, syag027. Doi: 10.1093/sysbio/syag027
  • Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30(4), 772–780. Doi: 10.1093/molbev/mst010
  • Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422. Doi: 10.1093/bioinformatics/btp163
  • Plotly Technologies Inc. (2015). Collaborative data science. Plotly Technologies Inc.

Acknowledgements

We wish to thank non-published softwares useful for EZmito2 development:

More
How to cite Project updates EZmito2 manual
ESZlab website