Overview of methods for studying adaptive introgression
| Method | Requires polarized data | Control panel | Target panel | Source panel | Additional data requirements |
|---|---|---|---|---|---|
| VolcanoFinder | No. | N/A | Phased or unphased genotypes. | N/A | Outgroup sequence to polarize ancestral states (optional). |
| Tutorial: Example workflow from Setter et al. (2020). | |||||
| genomatnn | No. | Phased or unphased genotypes. | Phased or unphased genotypes. | Phased or unphased genotypes. | Demographic history of the control, target, and source panels (at minimum). |
| Data: Pretrained models from Gower et al. (2021); Data: Adaptive introgression maps from Gower et al. (2021). | |||||
| MaLAdapt | Yes. | Phased genotypes. | Phased genotypes. | Phased or unphased genotypes. | Recombination map, genomic annotations (for computing exon density), and demographic history of the control, target, and source panels (at minimum). |
| Data: Adaptive introgression maps from Zhang et al. (2023). | |||||
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For each method, we provide a link to its documentation, note whether polarizing ancestral states is required, and describe the data requirements for a control panel (assumed to lack any genetic contributions from the source panel), a target panel (the putative recipient), and a source panel (the putative donor). We also provide any additional data requirements, along with links to publicly available resources (located in the second row per method) including published protocols and data sets. Note that the methods appear in the order in which they are referenced in the text, and all associated URL links are provided in the “Data sets” section.
