benjeffery

tsinfer-snakemake

A snakemake workflow for using tsinfer

administrative

project management documents and discussions for tskit development

bio2zarr

Convert bioinformatics file formats to Zarr

cyvcf2

cython + htslib == fast VCF and BCF processing

gel-upload

kastore

The key-array store for read-only numerical data.

msprime

A reimplementation of Hudson's classical ms simulator for modern data sets.

phylokit

Phylogenetics toolkit for the PyData Ecosystem

progen-2023

tskit poster for probgen 2023

pyodide

Pyodide is a Python distribution for the browser and Node.js based on WebAssembly

pyslim

Tools for dealing with tree sequences coming to and from SLiM.

sgkit

Statistical genetics toolkit

sgkit-publication

Sgkit publication repository

SLiM

SLiM is a genetically explicit forward simulation software package for population genetics and evolutionary biology. It is highly flexible, with a built-in scripting language, and has a cross-platform graphical modeling environment called SLiMgui.

tsconvert

Utilities for converting tree sequences to and from other formats

tsdate

Infer the age of ancestral nodes in a tree sequence

tsinfer

Infer a tree sequence from genetic variation data

tsinfer-feedstock

A conda-smithy repository for tsinfer.

tsinfer-qc

Utilities for evaluating tsinfer inferences

tskit

The tree sequence toolkit

tskit-book-theme

A book theme for documentation of tskit projects

tskit-feedstock

A conda-smithy repository for tskit.

tskit-paper

tskit-rust

Rust bindings for the tskit library

tskit-site

tskit website

tstrait

tszip

Gzip-like compression for tskit tree sequences

tutorials

A set of tutorials for msprime and tskit.

vcf-zarr-publication

Manuscript and associated scripts for vcf-zarr publication

zarr-python

An implementation of chunked, compressed, N-dimensional arrays for Python.