From 05ee69aa07ddad2d1a7e267982beac29ec4ccbfd Mon Sep 17 00:00:00 2001 From: Yan Wong Date: Tue, 10 Feb 2026 16:45:36 +0000 Subject: [PATCH] Add links to ARG inference software --- popgen.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/popgen.md b/popgen.md index 509192c..134c5f7 100644 --- a/popgen.md +++ b/popgen.md @@ -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).