The Mandrake program is described in:

Lees JA, Tonkin-Hill G, Yang Z, Corander J. Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation. 2021

The Stochestic Cluster Embedding algorithm was originally published in:

Yang, Zhirong, Yuwei Chen, Denis Sedov, Samuel Kaski, and Jukka Corander. 2021. “Stochastic Cluster Embedding.” arXiv [cs.LG]. arXiv.