News

Msprime 1.4 is a major feature release along with significant performance improvements.

The 1.0 release marks the coming-of-age of the tskit library. Breaking changes to tskit will not be made from now on (except in exceptional circumstances).

A pair of newly published papers describe efficient implementations of matrix-vector multiplication and principle component analysis in tskit, as well as ways to compare and infer haplotype lengths.

Duncan Robertson has worked on internal changes to tsinfer that greatly improve computational performance, now released as version 0.5.0

The 0.6.0 release of tskit is a major release with significant enhancements to genetic analysis capabilities, tree visualization, and general usability.

A new paper describing and justifying the tskit approach to encoding genetic ancestry was published in the journal Genetics.

Msprime 1.3.0 introduces the ability to record specific node types as well as edges for coalescing nodes along non-coalescing segments.

James Kitchens, a graduate student in the Coop lab in UC Davis, has released the first version of his D3-based javascript software for visualising Ancestral Recombination Graphs. Interactive plots of ARGs in tskit format can be created and displayed on web pages or in Jupyter notebooks.

Daiki Tagami, a student in the Kelleher group, has built tstrait, a software package to layer simulated quantitative phenotype traits on top of an existing tree sequence. This should be useful, for example, to create large simulated datasets for testing genome-wide association (GWAS) methods.

A trio of papers in the prestigious journals Nature, Science, and Nature Genetics illustrate the power of tskit-based simulation and analysis to carry out genome-wide analysis of human genome data. These focus on deep human ancestry, recent human pedigrees, and statistical algorithms for biobank-scale datasets.

Tsinfer 0.3.0 introduces a post-processing step that improves time estimation, allows alleles to be listed in any order, and exposes recombination and mismatch ratios to the command-line interface.

On Fri 30th Sept, an invited talk by Wilder Wohns focussing on results from recent tskit-related advances, for the online SMBE Everywhere symposium.

0.5.0 introduces balance metrics, tree arrays, topology operations, performance improvements and much more.

0.4.0 introduces reference sequences, virtual roots, extra space for data columns and much more.