Murillo F. Rodrigues

Hi, I would like to suggest for you to include a way to reorder the pages in the navbar. (if that is not implemented already)

sim_mutations and garbage collection

25

I'm pretty sure `sim_mutations` is accumulating some garbage same as pyslim (see [#pyslim211](https://github.com/tskit-dev/pyslim/issues/211#issue-1070866233)). Note how `sim_mutations` also calls `ts.tables`. I don't have the bandwidth right now to make a proper...

How do snakemake Modules work?

1

**Snakemake version** 6.10.0 **Describe the bug** From reading the docs I think I misunderstood what `Modules` do. I thought you could simply import a rule from a different Snakefile and...

add watterson's theta

8

this would be simple, as watterson's theta is ```ts.segregating_sites()/sum([1/i for i in range(1, ts.num_samples])```

unsure how SNPgenie does the polarization of mutations

1

Hi, It's not clear to me how SNPgenie polarizes the mutations (to compute dN/dS and piN/piS). Does it assume the ancestral states are the ones supplied in the reference fasta?...

wrap union to deal with SLiM metadata

4

e.g., by adjusting the slim mutation ids in the metadata, and the generation

Genome accessibility/callability

4

It is important to consider genome accessibility when computing rates from genomic data. scikit-allel has options to include an ["accessibility mask"](https://scikit-allel.readthedocs.io/en/stable/stats/diversity.html), a boolean array indicating whether a base is accessible...