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Add links to ARG inference software #297

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10 changes: 7 additions & 3 deletions popgen.md
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Expand Up @@ -260,9 +260,13 @@ plt.legend(handles=[
## Population genetic inference

If, instead of simulations, you want to analyse existing genomic data (for example
stored in a VCF file), you will need to infer a tree sequence from it, using e.g.
[tsinfer](https://tskit.dev/tsinfer/docs/stable/). Here we load an illustrative portion
of an [inferred tree sequence](https://zenodo.org/record/5512994)
stored in a VCF file), you will need to infer a tree sequence from it, using [ARG
inference software](https://www.patrickfournier.ca/arg-samplers-review/graph/#/page/arg%20inference) (such as [SINGER](https://github.com/popgenmethods/SINGER),
[Relate](https://myersgroup.github.io/relate/),
[Threads](https://github.com/PalamaraLab/threads), or
[tsinfer](https://github.com/tskit-dev/tsinfer)). Here we load an
illustrative portion of a tree sequence
[inferred by tsinfer+tsdate](https://zenodo.org/record/5512994) which is
based on about 7500 public human genomes, including genomes from the
[Thousand Genomes Project](https://www.internationalgenome.org/data-portal/data-collection/grch38) and
[Human Genome Diversity Project](https://www.internationalgenome.org/data-portal/data-collection/hgdp).
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