Verification Status

Disclaimer

The code examples in each Timepiece are verified by automated unit tests that re-implement the documented functions and check their mathematical properties. No Timepiece has been independently verified by a domain expert. If you find an error – mathematical, pedagogical, or computational – please open an issue. The table below shows the current verification status.

The Timepieces are grouped by what they do, with verification status for each.

Simulators – tools that generate ground truth

#	Timepiece	Tests	Verified	What it does
IV	msprime	190	–	Neutral coalescent with recombination. The clockwork that generates ground truth.
XVI	SLiM	67	–	Forward-time simulation with natural selection. The forge that builds what the coalescent cannot.
XVIII	discoal	132	–	Coalescent simulation with selective sweeps via trajectory + structured coalescent.

Demographic inference – estimating population size history

#	Timepiece	Tests	Verified	What it does
I	PSMC	186	–	Population size history from a single diploid genome. The simplest inference Timepiece.
II	SMC++	112	–	Extends PSMC to multiple unphased genomes with a distinguished lineage approach.
XIII	Gamma-SMC	107	–	Ultrafast pairwise TMRCA inference with gamma-distributed posteriors.
XIV	PHLASH	130	–	GPU-accelerated Bayesian inference of population size history via SVGD.

SFS-based demographic inference – using the site frequency spectrum

#	Timepiece	Tests	Verified	What it does
X	moments	162	–	Demographic inference from the SFS using moment equations.
XI	dadi	84	–	Demographic inference from the SFS by solving the Wright-Fisher diffusion PDE.
XII	momi2	140	–	Demographic inference from the SFS via coalescent tensor algebra.

Genealogy and ARG inference – reconstructing ancestral histories

#	Timepiece	Tests	Verified	What it does
III	Li & Stephens HMM	158	–	The copying model: a haplotype as a mosaic of references. A gear inside many Timepieces.
V	ARGweaver	120	–	Bayesian ARG sampling with discretized time. SINGER’s predecessor.
VI	tsinfer	142	–	Deterministic tree sequence inference at biobank scale.
VII	SINGER	172	–	Bayesian ARG sampling with continuous time and two-HMM architecture.
VIII	Threads	56	–	Deterministic ARG inference at biobank scale with PBWT pre-filtering.
XVII	Relate	66	–	Genome-wide genealogy estimation via asymmetric painting + MCMC branch lengths.

Dating and selection – calibrating genealogies and detecting selection

#	Timepiece	Tests	Verified	What it does
IX	tsdate	139	–	Dates tree sequence nodes using the molecular clock.
XV	CLUES	93	–	Full-likelihood estimation of selection coefficients from gene trees and ancient DNA.