PSMC+ – accurate demographic history reconstruction in the presence of background selection (Cousins et al 2024 bioRxiv)
MalAdapt – Extra-trees based classifier for detecting adaptive archaic introgression (Zhang et al 2023 Molecular Biology and Evolution)
OrientAGraph – Maximum likelihood network orientation for admixture graphs (Molloy et al 2021 Bioinformatics)
Archaic local ancestry calls for YRI and MSL (Durvasula et al 2020 Science Advances)
ArchIE – Reference-free inference of archaic local ancestry (Durvasula et al 2019 PLoS Genetics)
ANGSD-wrapper – Utilities for analyzing next generation sequencing data (Durvasula et al 2016 Molecular Ecology Resources)