 _____ _____                      
| ____|__  /_ __   ___ ___   __ _ 
|  _|   / /| '_ \ / __/ _ \ / _` |
| |___ / /_| |_) | (_| (_) | (_| |
|_____/____| .__/ \___\___/ \__,_|
           |_|


Starting EZpcoa run
FASTA      : /home/labadmin/Ezmito/uploaded_jobs/claudio_20260626_192945_532744_f2c38566/Ezpcoa.fasta
Pop map    : /home/labadmin/Ezmito/uploaded_jobs/claudio_20260626_192945_532744_f2c38566/Ezpcoa.popmap.tsv
Method     : PCoA
Dist model : K2P
Components : 3
Palette    : Dark2

Sequences: 41  |  Length: 1225 bp
Clean columns: 1225 / 1225  |  IUPAC chars: 8 (skipped in pairwise)
Population map loaded: 41 entries
Populations: ['CCI', 'CHA', 'CJO', 'COI', 'MCI', 'RCR']

Computing K2P pairwise distance matrix (41×41)...
Distance range: 0.025890  mean: 0.013235
Running PCoA (classical MDS)...
PCoA complete. Variance explained: PC1=66.7% | PC2=20.6% | PC3=3.7%
Coordinates saved: pcoa_coordinates.tsv
Generating plots ...
Unique haplotypes: 39
Saved: PCOA_PC1_PC2.pdf
Saved: PCOA_all_pairs.pdf
Saved: PCOA_screeplot.pdf

Total runtime: 2.65 seconds

Citations
---------
If you used this tool, please cite:

- Cucini, C., Leo, C., Iannotti, N., Boschi, S., Brunetti, C., Pons, J., Fanciulli, P.P., Frati, F., Carapelli, A., & Nardi, F. (2021). EZmito: a simple and fast tool for multiple mitogenome analyses. Mitochondrial DNA Part B, 6(3), 1101-1109. https://doi.org/10.1080/23802359.2021.1899865


- 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. https://doi.org/10.1007/bf01731581
- Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in science & engineering, 9(3), 90-95. https://doi.org/10.1109/MCSE.2007.55
- McKinney, W. (2010). Data structures for statistical computing in Python. 445(1), 51-56. https://doi.org/10.25080/Majora-92bf1922-00a
