References

Software

Reference

PhyloDM

Aaron Mussig. aaronmussig/PhyloDM. Zenodo, doi: 10.5281/zenodo.3998716

DendroPy

Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571, doi: 10.1093/bioinformatics/btq228

NumPy

Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020), doi: 10.1038/s41586-020-2649-2

tqdm

Casper da Costa-Luis, et al. tqdm: A fast, Extensible Progress Bar for Python and CLI. Zenodo, doi: 10.5281/zenodo.595120

ETE 3

ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016, doi: 10.1093/molbev/msw046

Matplotlib

    1. Hunter, “Matplotlib: A 2D Graphics Environment,” in Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, May-June 2007, doi: 10.1109/MCSE.2007.55

Method

Reference

Theil-Sen Estimator

Theil, H. (1992). A Rank-Invariant Method of Linear and Polynomial Regression Analysis. In B. Raj & J. Koerts (Eds.), Henri Theil’s Contributions to Economics and Econometrics: Econometric Theory and Methodology (pp. 345–381). Springer Netherlands. 10.1007/978-94-011-2546-8_20

Sen, P. K. (1968). Estimates of the Regression Coefficient Based on Kendall’s Tau. Journal of the American Statistical Association, 63(324), 1379–1389. 10.1080/01621459.1968.10480934

Jackknife-After-Bootstrap

Efron, B. (1992). Jackknife-After-Bootstrap Standard Errors and Influence Functions. Journal of the Royal Statistical Society. Series B (Methodological), 54(1), 83–127. JSTOR.