PAICE (Phylogeographic Analysis of Island Colonization Events) is a haplotype-based method implemented into an R package to estimate the number of inter-island colonization events between the islands of an archipelago. Although designed for oceanic archipelagos, it works in any island-like system (e.g., sky islands). For further information, check our publication in Journal of Biogeography (Coello et al. 2022).
A complete guide can be found on our Wiki.