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The Workshop
The Watchmaker’s Philosophy
The Workbench (Prerequisites)
The Workbench (Prerequisites)
Likelihood-Based Probabilistic Inference
Coalescent Theory
Ancestral Recombination Graphs
Hidden Markov Models
The Sequentially Markov Coalescent
The Diffusion Approximation
Ordinary Differential Equations
Markov Chain Monte Carlo
Timepieces
Timepieces
Verification Status
Timepiece I: PSMC
Overview of PSMC
The Continuous-Time PSMC Model
Discretizing Time
The PSMC HMM and EM Algorithm
Decoding the Clock
Demo: Running PSMC on Simulated Data
Timepiece II: SMC++
Overview of SMC++
The Distinguished Lineage
The ODE System
The Continuous HMM
Population Splits
Demo: Running SMC++ on Simulated Data
Timepiece III: The Li & Stephens HMM
Overview of the Li & Stephens HMM
The Copying Model
Haploid LS HMM Algorithms
The Diploid Extension
Demo: Running the Li & Stephens HMM on Simulated Data
Timepiece IV: msprime
Overview of msprime
The Coalescent Process
Segments & the Fenwick Tree
Hudson’s Algorithm
Demographics & Population
Mutations
Demo: Running msprime on Simulated Data
Timepiece V: ARGweaver
Overview of ARGweaver
Time Discretization
Transition Probabilities
Emission Probabilities
MCMC Sampling
Demo: Running ARGweaver on Simulated Data
Timepiece VI: tsinfer
Overview of tsinfer
Gear 1: Ancestor Generation
Gear 2: The Copying Model
Gear 3: Ancestor Matching
Gear 4: Sample Matching & Post-Processing
Demo: Running tsinfer on Simulated Data
Timepiece VII: SINGER
Overview of SINGER
Branch Sampling
Time Sampling
ARG Rescaling
Sub-Graph Pruning and Re-grafting (SGPR)
Demo: Running SINGER on Simulated Data
Timepiece VIII: Threads
Overview of Threads
Haplotype Matching with the PBWT
Memory-Efficient Viterbi Inference
Dating Path Segments
Demo: Running Threads on Simulated Data
Timepiece IX: tsdate
Overview of tsdate
The Coalescent Prior
The Mutation Likelihood
Inside-Outside Belief Propagation
Variational Gamma (Expectation Propagation)
Rescaling
Demo: Running tsdate on Simulated Data
Timepiece X: moments
Overview of moments
The Site Frequency Spectrum
The Moment Equations
Demographic Inference
Linkage Disequilibrium
Demo: Running moments on Simulated Data
Timepiece XI: dadi
Overview of dadi
The Diffusion Equation
Numerical Integration
Demographic Inference
Demo: Running dadi on Simulated Data
Timepiece XII: momi2
Overview of momi2
The Coalescent SFS
The Moran Model
Tensor Machinery
Automatic Differentiation & Inference
Demo: Running momi2 on Simulated Data
Timepiece XIII: Gamma-SMC
Overview of Gamma-SMC
The Gamma Approximation
The Flow Field
The Forward-Backward CS-HMM
Segmentation and Caching
Demo: Running Gamma-SMC on Simulated Data
Timepiece XIV: PHLASH
Overview of PHLASH
The Composite Likelihood
Random Time Discretization
The Score Function Algorithm
Stein Variational Gradient Descent (SVGD)
Demo: Running PHLASH on Simulated Data
Timepiece XV: CLUES
Overview: Detecting Selection
The Wright-Fisher HMM
Emission Probabilities
Inference: From Gene Trees to Selection
Demo: Running CLUES on Simulated Data
Timepiece XVI: SLiM
Overview of SLiM
The Wright-Fisher Generation Cycle
Recipes
Demo: Running SLiM on Simulated Data
Timepiece XVII: Relate
Overview of Relate
Gear 1: Asymmetric Painting
Gear 2: Tree Building
Gear 3: Branch Length Estimation (MCMC)
Gear 4: Population Size Estimation
Demo: Running Relate on Simulated Data
Timepiece XVIII: discoal
Overview of discoal
The Allele Frequency Trajectory
The Structured Coalescent Under Selection
Hard, Soft, and Partial Sweeps
discoal and msprime: Two Takes on Sweeps
Demo: Running discoal on Simulated Data
Index
