jeromekelleher

phylokit

Phylogenetics toolkit for the PyData Ecosystem

sc2ts

Infer a succinct tree sequence from SARS-COV-2 variation data

sc2ts-paper

cyvcf2

cython + htslib == fast VCF and BCF processing

tsinfer

Infer a tree sequence from genetic variation data

tskit

The tree sequence toolkit

adding-species-manuscript

manuscript materials for the adding species paper

bed-reader-feedstock

A conda-smithy repository for bed-reader.

bio2zarr

Convert bioinformatics file formats to Zarr

divmat

ga4gh-client-c

Experimental C client library for the GA4GH API.

kastore

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

lshmm

code to run Li and Stephens

msprime

Simulate genealogical trees and genomic sequence data using population genetic models

progen-2023

tskit poster for probgen 2023

sgkit

Statistical genetics toolkit

sgkit-feedstock

A conda-smithy repository for sgkit.

sgkit-publication

Sgkit publication repository

slim-feedstock

A conda-smithy repository for slim.

smc-bit-paper

Paper on backwards in time SMC description

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

stdpopsim-feedstock

A conda-smithy repository for stdpopsim.

tsinfer-qc

Utilities for evaluating tsinfer inferences

tskit-site

tskit website

tstrait

tstrait-paper

vcf-zarr-publication

Manuscript and associated scripts for vcf-zarr publication

vcztools

Partial reimplementation of bcftools for VCF Zarr

what-is-an-arg-paper

Manuscript and code for the "What is an ARG?" paper

wormtable

Write-once-read-many table for large datasets.