Mandrake paper:

Lees JA, Tonkin-Hill G, Yang Z, Corander J. Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation. Philosophical Transactions of The Royal Society B. 2022;377: 20210237.

Stochastic Cluster Embedding paper:

Yang Z, Chen Y, Sedov D, Kaski S, Corander J. Stochastic cluster embedding. Stat Comput 33, 12 (2023).

Original SCE code: