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Efficient ancestry and mutation simulation with msprime 1.0

https://doi.org/10.1093/genetics/iyab229

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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/gepi.21876openalex-snapshot

Genetic Data Simulators and their Applications: An Overview

inferredcites →https://doi.org/10.1006/tpbi.1998.1403openalex-snapshot

Recombination as a Point Process along Sequences

inferredcites →https://doi.org/10.1007/978-1-0716-0199-0_9openalex-snapshot

Coalescent Simulation with msprime

inferredcites →https://doi.org/10.1007/978-1-4615-2383-3_15openalex-snapshot

Mitochondrial Haplotype Frequencies in Oysters: Neutral Alternatives to Selection Models

inferredcites →https://doi.org/10.1007/bf00168175openalex-snapshot

On the two-locus sampling distribution

inferredcites →https://doi.org/10.1007/bf01731581openalex-snapshot

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

inferredcites →https://doi.org/10.1007/s00285-020-01470-5openalex-snapshot

Cannings models, population size changes and multiple-merger coalescents

inferredcites →https://doi.org/10.1007/s10955-018-2013-1openalex-snapshot

Genealogical Properties of Subsamples in Highly Fecund Populations

inferredcites →https://doi.org/10.1007/s11222-009-9116-0openalex-snapshot

Non-linear regression models for Approximate Bayesian Computation

inferredcites →https://doi.org/10.1016/0040-5809(83)90013-8openalex-snapshot

Properties of a neutral allele model with intragenic recombination

inferredcites →https://doi.org/10.1016/0040-5809(85)90036-xopenalex-snapshot

The use of sample genealogies for studying a selectively neutral m-loci model with recombination

inferredcites →https://doi.org/10.1016/0304-4149(82)90011-4openalex-snapshot

The coalescent

inferredcites →https://doi.org/10.1016/b978-1-4832-3211-9.50009-7openalex-snapshot

Evolution of Protein Molecules

inferredcites →https://doi.org/10.1016/j.ajhg.2017.03.004openalex-snapshot

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

inferredcites →https://doi.org/10.1016/j.ajhg.2020.08.017openalex-snapshot

Lessons Learned from Bugs in Models of Human History

inferredcites →https://doi.org/10.1016/j.ajhg.2020.08.020openalex-snapshot

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

inferredcites →https://doi.org/10.1016/j.ajhg.2021.09.006openalex-snapshot

Revisiting the out of Africa event with a deep-learning approach

inferredcites →https://doi.org/10.1016/j.mbs.2019.03.004openalex-snapshot

Robust model selection between population growth and multiple merger coalescents

inferredcites →https://doi.org/10.1016/j.softx.2018.09.003openalex-snapshot

SimPrily: A Python framework to simplify high-throughput genomic simulations

inferredcites →https://doi.org/10.1016/j.tig.2017.12.005openalex-snapshot

Supervised Machine Learning for Population Genetics: A New Paradigm

inferredcites →https://doi.org/10.1016/j.tpb.2004.04.002openalex-snapshot

Approximating selective sweeps

inferredcites →https://doi.org/10.1016/j.tpb.2004.06.006openalex-snapshot

Ancestral inference on gene trees under selection

inferredcites →https://doi.org/10.1016/j.tpb.2014.01.002openalex-snapshot

Markovian approximation to the finite loci coalescent with recombination along multiple sequences

inferredcites →https://doi.org/10.1016/j.tpb.2014.05.001openalex-snapshot

Coalescent simulation in continuous space: Algorithms for large neighbourhood size

inferredcites →https://doi.org/10.1016/j.tpb.2016.04.002openalex-snapshot

The site-frequency spectrum associated with Ξ -coalescents

inferredcites →https://doi.org/10.1016/j.tpb.2017.10.002openalex-snapshot

Evolution of highly fecund haploid populations

inferredcites →https://doi.org/10.1016/j.tpb.2019.02.001openalex-snapshot

Phase-type distributions in population genetics

inferredcites →https://doi.org/10.1016/j.tree.2010.04.001openalex-snapshot

Approximate Bayesian Computation (ABC) in practice

inferredcites →https://doi.org/10.1016/s0140-6736(18)33135-0openalex-snapshot

Gender equality in science, medicine, and global health: where are we at and why does it matter?

inferredcites →https://doi.org/10.1016/s0304-4149(03)00028-0openalex-snapshot

Coalescent processes obtained from supercritical Galton–Watson processes

inferredcites →https://doi.org/10.1017/s0021900200034446openalex-snapshot

On the genealogy of large populations

inferredcites →https://doi.org/10.1038/hdy.2013.38openalex-snapshot

A sequential coalescent algorithm for chromosomal inversions

inferredcites →https://doi.org/10.1038/hdy.2016.58openalex-snapshot

On the importance of skewed offspring distributions and background selection in virus population genetics

inferredcites →https://doi.org/10.1038/nature10231openalex-snapshot

Inference of human population history from individual whole-genome sequences

inferredcites →https://doi.org/10.1038/ng.3015openalex-snapshot

Inferring human population size and separation history from multiple genome sequences

inferredcites →https://doi.org/10.1038/ng.3748openalex-snapshot

Robust and scalable inference of population history from hundreds of unphased whole genomes

inferredcites →https://doi.org/10.1038/nrg2193openalex-snapshot

Gene conversion: mechanisms, evolution and human disease

inferredcites →https://doi.org/10.1038/nrg3130openalex-snapshot

Computer simulations: tools for population and evolutionary genetics

inferredcites →https://doi.org/10.1038/s10038-020-00862-1openalex-snapshot

Practical guide for managing large-scale human genome data in research

inferredcites →https://doi.org/10.1038/s41437-017-0005-6openalex-snapshot

The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

inferredcites →https://doi.org/10.1038/s41586-018-0579-zopenalex-snapshot

The UK Biobank resource with deep phenotyping and genomic data

inferredcites →https://doi.org/10.1038/s41586-020-2308-7openalex-snapshot

The mutational constraint spectrum quantified from variation in 141,456 humans

inferredcites →https://doi.org/10.1038/s41586-020-2547-7openalex-snapshot

Telomere-to-telomere assembly of a complete human X chromosome

inferredcites →https://doi.org/10.1038/s41586-020-2649-2openalex-snapshot

Array programming with NumPy

inferredcites →https://doi.org/10.1038/s41588-019-0483-yopenalex-snapshot

Inferring whole-genome histories in large population datasets

inferredcites →https://doi.org/10.1038/s41588-019-0484-xopenalex-snapshot

A method for genome-wide genealogy estimation for thousands of samples

inferredcites →https://doi.org/10.1038/s41588-019-0492-xopenalex-snapshot

From a database of genomes to a forest of evolutionary trees

inferredcites →https://doi.org/10.1038/s41588-021-00862-7openalex-snapshot

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic

inferredcites →https://doi.org/10.1038/s41592-019-0639-9openalex-snapshot

Genealogy at the genome scale

inferredcites →https://doi.org/10.1038/s41598-018-27891-3openalex-snapshot

Recovery of coral assemblages despite acute and recurrent disturbances on a South Central Pacific reef

inferredcites →https://doi.org/10.1038/s41598-018-28539-yopenalex-snapshot

Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference

inferredcites →https://doi.org/10.1073/pnas.1213113110openalex-snapshot

Genealogies of rapidly adapting populations

inferredcites →https://doi.org/10.1073/pnas.1322709111openalex-snapshot

Distortion of genealogical properties when the sample is very large

inferredcites →https://doi.org/10.1073/pnas.78.1.454openalex-snapshot

Estimation of evolutionary distances between homologous nucleotide sequences.

inferredcites →https://doi.org/10.1073/pnas.89.22.10915openalex-snapshot

Amino acid substitution matrices from protein blocks.

inferredcites →https://doi.org/10.1080/01621459.2019.1635482openalex-snapshot

Efficiently Inferring the Demographic History of Many Populations With Allele Count Data

inferredcites →https://doi.org/10.1086/508901openalex-snapshot

Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs

inferredcites →https://doi.org/10.1089/cmb.2010.0188openalex-snapshot

An Overview of Population Genetic Data Simulation

inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

inferredcites →https://doi.org/10.1093/bioinformatics/18.2.337openalex-snapshot

Generating samples under a Wright–Fisher neutral model of genetic variation

inferredcites →https://doi.org/10.1093/bioinformatics/btaa090openalex-snapshot

Occupancy spectrum distribution: application for coalescence simulation with generic mergers

inferredcites →https://doi.org/10.1093/bioinformatics/btaa486openalex-snapshot

ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network

inferredcites →https://doi.org/10.1093/bioinformatics/btab261openalex-snapshot

GSpace: an exact coalescence simulator of recombining genomes under isolation by distance

inferredcites →https://doi.org/10.1093/bioinformatics/bth417openalex-snapshot

SelSim: a program to simulate population genetic data with natural selection and recombination

inferredcites →https://doi.org/10.1093/bioinformatics/bti1200openalex-snapshot

DNA assembly with gaps (Dawg): simulating sequence evolution

inferredcites →https://doi.org/10.1093/bioinformatics/btl415openalex-snapshot

Nemo: an evolutionary and population genetics programming framework

inferredcites →https://doi.org/10.1093/bioinformatics/btl622openalex-snapshot

msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots

inferredcites →https://doi.org/10.1093/bioinformatics/btn514openalex-snapshot

Inferring population history withDIY ABC: a user-friendly approach to approximate Bayesian computation

inferredcites →https://doi.org/10.1093/bioinformatics/btp487openalex-snapshot

PopABC: a program to infer historical demographic parameters

inferredcites →https://doi.org/10.1093/bioinformatics/btq322openalex-snapshot

MSMS : a coalescent simulation program including recombination, demographic structure and selection at a single locus

inferredcites →https://doi.org/10.1093/bioinformatics/btr124openalex-snapshot

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

inferredcites →https://doi.org/10.1093/bioinformatics/btt067openalex-snapshot

Coalescent simulation in continuous space

inferredcites →https://doi.org/10.1093/bioinformatics/btu562openalex-snapshot

Cosi2: an efficient simulator of exact and approximate coalescent with selection

inferredcites →https://doi.org/10.1093/bioinformatics/btu861openalex-snapshot

scrm: efficiently simulating long sequences using the approximated coalescent with recombination

inferredcites →https://doi.org/10.1093/bioinformatics/btv684openalex-snapshot

Reliable ABC model choice via random forests

inferredcites →https://doi.org/10.1093/bioinformatics/btw098openalex-snapshot

Coala: an R framework for coalescent simulation

inferredcites →https://doi.org/10.1093/bioinformatics/btw355openalex-snapshot

ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process

inferredcites →https://doi.org/10.1093/bioinformatics/btw556openalex-snapshot

Discoal: flexible coalescent simulations with selection

inferredcites →https://doi.org/10.1093/bioinformatics/bty867openalex-snapshot

ABC random forests for Bayesian parameter inference

inferredcites →https://doi.org/10.1093/g3journal/jkaa017openalex-snapshot

AlphaSimR: an R package for breeding program simulations

inferredcites →https://doi.org/10.1093/genetics/105.2.437openalex-snapshot

EVOLUTIONARY RELATIONSHIP OF DNA SEQUENCES IN FINITE POPULATIONS

inferredcites →https://doi.org/10.1093/genetics/123.4.887openalex-snapshot

The "hitchhiking effect" revisited.

inferredcites →https://doi.org/10.1093/genetics/134.4.1289openalex-snapshot

The effect of deleterious mutations on neutral molecular variation.

inferredcites →https://doi.org/10.1093/genetics/140.2.783openalex-snapshot

The hitchhiking effect on the site frequency spectrum of DNA polymorphisms.

inferredcites →https://doi.org/10.1093/genetics/141.4.1619openalex-snapshot

The pattern of neutral molecular variation under the background selection model.

inferredcites →https://doi.org/10.1093/genetics/151.3.1217openalex-snapshot

The Ancestry of a Sample of Sequences Subject to Recombination

inferredcites →https://doi.org/10.1093/genetics/154.2.931openalex-snapshot

Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms

inferredcites →https://doi.org/10.1093/genetics/155.1.451openalex-snapshot

The Coalescent With Gene Conversion

inferredcites →https://doi.org/10.1093/genetics/155.2.909openalex-snapshot

Genetic Drift in an Infinite Population: The Pseudohitchhiking Model

inferredcites →https://doi.org/10.1093/genetics/155.2.981openalex-snapshot

Detecting Bottlenecks and Selective Sweeps From DNA Sequence Polymorphism

inferredcites →https://doi.org/10.1093/genetics/156.3.1393openalex-snapshot

Maximum Likelihood Estimation of Recombination Rates From Population Data

inferredcites →https://doi.org/10.1093/genetics/160.2.765openalex-snapshot

Detecting a Local Signature of Genetic Hitchhiking Along a Recombining Chromosome

inferredcites →https://doi.org/10.1093/genetics/162.4.2025openalex-snapshot

Approximate Bayesian Computation in Population Genetics

inferredcites →https://doi.org/10.1093/genetics/166.4.1871openalex-snapshot

Mitochondrial Cytochrome b DNA Variation in the High-Fecundity Atlantic Cod: Trans-Atlantic Clines and Shallow Gene Genealogy

inferredcites →https://doi.org/10.1093/genetics/iyac131openalex-snapshot

Demes: a standard format for demographic models

inferredcites →https://doi.org/10.1093/molbev/msaa038openalex-snapshot

Predicting the Landscape of Recombination Using Deep Learning

inferredcites →https://doi.org/10.1093/molbev/msab174openalex-snapshot

Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies

inferredcites →https://doi.org/10.1093/molbev/msab175openalex-snapshot

Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations

inferredcites →https://doi.org/10.1093/molbev/msab264openalex-snapshot

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot

INDELible: A Flexible Simulator of Biological Sequence Evolution

inferredcites →https://doi.org/10.1093/molbev/msp274openalex-snapshot

Bayesian Inference of Species Trees from Multilocus Data

inferredcites →https://doi.org/10.1093/molbev/msw048openalex-snapshot

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

inferredcites →https://doi.org/10.1093/molbev/msw283openalex-snapshot

Archaic adaptive introgression in TBX15/WARS2

inferredcites →https://doi.org/10.1093/molbev/msy224openalex-snapshot

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference

inferredcites →https://doi.org/10.1093/molbev/msy228openalex-snapshot

SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model

inferredcites →https://doi.org/10.1093/oso/9780198529958.001.0001openalex-snapshot

Gene Genealogies, Variation and Evolution

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025575openalex-snapshot

A Hidden Markov Model approach to variation among sites in rate of evolution

inferredcites →https://doi.org/10.1098/rstb.1994.0079openalex-snapshot

Sampling theory for neutral alleles in a varying environment

inferredcites →https://doi.org/10.1098/rstb.2005.1673openalex-snapshot

Approximating the coalescent with recombination

inferredcites →https://doi.org/10.1098/rstb.2008.0172openalex-snapshot

Bayesian inference of fine-scale recombination rates using population genomic data

inferredcites →https://doi.org/10.1099/mgen.0.000044openalex-snapshot

SimBac: simulation of whole bacterial genomes with homologous recombination

inferredcites →https://doi.org/10.1101/2021.10.27.466171openalex-snapshot

Recommendations for improving statistical inference in population genomics

inferredcites →https://doi.org/10.1101/267211openalex-snapshot

A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks

inferredcites →https://doi.org/10.1101/gr.083634.108openalex-snapshot

Fast and flexible simulation of DNA sequence data

inferredcites →https://doi.org/10.1111/1755-0998.12607openalex-snapshot

skelesim : an extensible, general framework for population genetic simulation in R

inferredcites →https://doi.org/10.1111/1755-0998.12968openalex-snapshot

Tree‐sequence recording in SLiM opens new horizons for forward‐time simulation of whole genomes

inferredcites →https://doi.org/10.1111/1755-0998.12992openalex-snapshot

The Quetzal Coalescence template library: A C++ programmers resource for integrating distributional, demographic and coalescent models

inferredcites →https://doi.org/10.1111/1755-0998.13163openalex-snapshot

Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data

inferredcites →https://doi.org/10.1111/1755-0998.13224openalex-snapshot

Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation

inferredcites →https://doi.org/10.1111/eva.12343openalex-snapshot

Women in evolution – highlighting the changing face of evolutionary biology

inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb00188.xopenalex-snapshot

THE ECOLOGY AND GENETICS OF FITNESS IN CHLAMYDOMONAS. XII. REPEATED SEXUAL EPISODES INCREASE RATES OF ADAPTATION TO NOVEL ENVIRONMENTS

inferredcites →https://doi.org/10.1111/j.1558-5646.1983.tb05528.xopenalex-snapshot

TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA

inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01019.xopenalex-snapshot

A NEW MODEL FOR EXTINCTION AND RECOLONIZATION IN TWO DIMENSIONS: QUANTIFYING PHYLOGEOGRAPHY

inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02832.xopenalex-snapshot

msABC: a modification of Hudson’s ms to facilitate multi‐locus ABC analysis

inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00179.xopenalex-snapshot

abc: an R package for approximate Bayesian computation (ABC)

inferredcites →https://doi.org/10.1111/mec.13610openalex-snapshot

Powerful methods for detecting introgressed regions from population genomic data

inferredcites →https://doi.org/10.1111/mec.13736openalex-snapshot

Gene conversion and linkage: effects on genome evolution and speciation

inferredcites →https://doi.org/10.1126/sciadv.aaw9206openalex-snapshot

Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

inferredcites →https://doi.org/10.1126/sciadv.abc0776openalex-snapshot

An ancestral recombination graph of human, Neanderthal, and Denisovan genomes

inferredcites →https://doi.org/10.1126/sciadv.abj4713openalex-snapshot

Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner

inferredcites →https://doi.org/10.1126/science.abi8264openalex-snapshot

A unified genealogy of modern and ancient genomes

inferredcites →https://doi.org/10.1146/annurev-ecolsys-010621-044528openalex-snapshot

Effects of Selection at Linked Sites on Patterns of Genetic Variability

inferredcites →https://doi.org/10.1186/1471-2105-10-166openalex-snapshot

mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

inferredcites →https://doi.org/10.1186/1471-2105-11-1openalex-snapshot

Detection of gene pathways with predictive power for breast cancer prognosis

inferredcites →https://doi.org/10.1186/1471-2105-11-116openalex-snapshot

ABCtoolbox: a versatile toolkit for approximate Bayesian computations

inferredcites →https://doi.org/10.1186/1471-2105-12-1openalex-snapshot

MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity

inferredcites →https://doi.org/10.1186/1471-2105-15-273openalex-snapshot

A new method for modeling coalescent processes with recombination

inferredcites →https://doi.org/10.1186/1471-2105-15-3openalex-snapshot

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences

inferredcites →https://doi.org/10.1186/1471-2105-6-1openalex-snapshot

A novel method for prokaryotic promoter prediction based on DNA stability

inferredcites →https://doi.org/10.1186/1471-2105-6-252openalex-snapshot

CoaSim: A flexible environment for simulating genetic data under coalescent models

inferredcites →https://doi.org/10.1186/1471-2105-8-1openalex-snapshot

Comparing sequences without using alignments: application to HIV/SIV subtyping

inferredcites →https://doi.org/10.1186/1471-2105-8-268openalex-snapshot

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation

inferredcites →https://doi.org/10.1186/1471-2105-8-458openalex-snapshot

Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography

inferredcites →https://doi.org/10.1186/1471-2156-7-16openalex-snapshot

Fast "coalescent" simulation

inferredcites →https://doi.org/10.1186/1479-7364-3-1-79openalex-snapshot

A survey of genetic simulation software for population and epidemiological studies

inferredcites →https://doi.org/10.1186/s12859-015-0721-yopenalex-snapshot

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

inferredcites →https://doi.org/10.1186/s13059-019-1763-7openalex-snapshot

Challenges in funding and developing genomic software: roots and remedies

inferredcites →https://doi.org/10.1186/s13059-022-02625-xopenalex-snapshot

Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software

inferredcites →https://doi.org/10.1214/17-ejp58openalex-snapshot

Rigorous results for a population model with selection II: genealogy of the population

inferredcites →https://doi.org/10.1214/18-ejp175openalex-snapshot

Coalescent results for diploid exchangeable population models

inferredcites →https://doi.org/10.1214/aop/1015345761openalex-snapshot

A Classification of Coalescent Processes for Haploid Exchangeable Population Models

inferredcites →https://doi.org/10.1214/aop/1022677258openalex-snapshot

Particle Representations for Measure-Valued Population Models

inferredcites →https://doi.org/10.1214/aop/1022874819openalex-snapshot

Coalescents With Multiple Collisions

inferredcites →https://doi.org/10.1214/ejp.v19-2642openalex-snapshot

The infinitely many genes model with horizontal gene transfer

inferredcites →https://doi.org/10.1214/ejp.v5-68openalex-snapshot

Coalescents with Simultaneous Multiple Collisions

inferredcites →https://doi.org/10.1214/lnms/1215459289openalex-snapshot

The Two-Locus Ancestral Graph

inferredcites →https://doi.org/10.1239/jap/1032374759openalex-snapshot

The general coalescent with asynchronous mergers of ancestral lines

inferredcites →https://doi.org/10.1371/journal.pbio.3001669openalex-snapshot

Recommendations for improving statistical inference in population genomics

inferredcites →https://doi.org/10.1371/journal.pcbi.1002495openalex-snapshot

Simulation of Molecular Data under Diverse Evolutionary Scenarios

inferredcites →https://doi.org/10.1371/journal.pcbi.1004842openalex-snapshot

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

inferredcites →https://doi.org/10.1371/journal.pcbi.1004845openalex-snapshot

Deep Learning for Population Genetic Inference

inferredcites →https://doi.org/10.1371/journal.pcbi.1005134openalex-snapshot

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology

inferredcites →https://doi.org/10.1371/journal.pcbi.1006526openalex-snapshot

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

inferredcites →https://doi.org/10.1371/journal.pcbi.1006581openalex-snapshot

Efficient pedigree recording for fast population genetics simulation

inferredcites →https://doi.org/10.1371/journal.pcbi.1010056openalex-snapshot

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets

inferredcites →https://doi.org/10.1371/journal.pgen.0020166openalex-snapshot

Inferring the Demographic History and Rate of Adaptive Substitution in Drosophila

inferredcites →https://doi.org/10.1371/journal.pgen.1004342openalex-snapshot

Genome-Wide Inference of Ancestral Recombination Graphs

inferredcites →https://doi.org/10.1371/journal.pgen.1008552openalex-snapshot

Tracking human population structure through time from whole genome sequences

inferredcites →https://doi.org/10.1371/journal.pgen.1008619openalex-snapshot

Accounting for long-range correlations in genome-wide simulations of large cohorts

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What is ancestry?

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inferred← citeshttps://doi.org/10.1093/genetics/iyae103openalex-snapshot

Single nucleotide polymorphism profile for quantitative trait nucleotide in populations with small effective size and its impact on mapping and genomic predictions

inferred← citeshttps://doi.org/10.1093/genetics/iyae110openalex-snapshot

Testing times: disentangling admixture histories in recent and complex demographies using ancient DNA

inferred← citeshttps://doi.org/10.1093/genetics/iyae134openalex-snapshot

The geometry of admixture in population genetics: the blessing of dimensionality

inferred← citeshttps://doi.org/10.1093/genetics/iyae144openalex-snapshot

An explanation for the sister repulsion phenomenon in Patterson's f -statistics

inferred← citeshttps://doi.org/10.1093/genetics/iyae157openalex-snapshot

Genealogical asymmetry under the IM model and a two-taxon test for gene flow

inferred← citeshttps://doi.org/10.1093/genetics/iyae180openalex-snapshot

Population size rescaling significantly biases outcomes of forward-in-time population genetic simulations

inferred← citeshttps://doi.org/10.1093/genetics/iyae182openalex-snapshot

A path integral approach for allele frequency dynamics under polygenic selection

inferred← citeshttps://doi.org/10.1093/genetics/iyae210openalex-snapshot

Characterizing selection on complex traits through conditional frequency spectra

inferred← citeshttps://doi.org/10.1093/genetics/iyae212openalex-snapshot

Estimating effective population size trajectories from time-series identity-by-descent segments

inferred← citeshttps://doi.org/10.1093/genetics/iyaf004openalex-snapshot

High-recombining genomic regions affect demography inference based on ancestral recombination graphs

inferred← citeshttps://doi.org/10.1093/genetics/iyaf023openalex-snapshot

Detecting deviations from Kingman coalescence using 2-site frequency spectra

inferred← citeshttps://doi.org/10.1093/genetics/iyaf034openalex-snapshot

Error rates in QST–FST comparisons depend on genetic architecture and estimation procedures

inferred← citeshttps://doi.org/10.1093/genetics/iyaf047openalex-snapshot

Performance of qpAdm -based screens for genetic admixture on graph–shaped histories and stepping stone landscapes

inferred← citeshttps://doi.org/10.1093/genetics/iyaf094openalex-snapshot

A rapid accurate approach to inferring pedigrees in endogamous populations

inferred← citeshttps://doi.org/10.1093/genetics/iyaf103openalex-snapshot

Likelihoods for a general class of ARGs under the SMC

inferred← citeshttps://doi.org/10.1093/genetics/iyaf135openalex-snapshot

PhaseGen: exact solutions for time-inhomogeneous multivariate coalescent distributions under diverse demographies

inferred← citeshttps://doi.org/10.1093/genetics/iyaf181openalex-snapshot

A model-free method for genealogical inference without phasing and its application for topology weighting

inferred← citeshttps://doi.org/10.1093/genetics/iyaf183openalex-snapshot

Signatures of selective sweeps in continuous-space populations

inferred← citeshttps://doi.org/10.1093/genetics/iyaf198openalex-snapshot

A forest is more than its trees: haplotypes and ancestral recombination graphs

inferred← citeshttps://doi.org/10.1093/genetics/iyaf204openalex-snapshot

Mutation ages and population origins inferred from genomes in structured populations

inferred← citeshttps://doi.org/10.1093/genetics/iyaf219openalex-snapshot

On ARGs, pedigrees, and genetic relatedness matrices

inferred← citeshttps://doi.org/10.1093/genetics/iyaf244openalex-snapshot

Optimizing genomic sampling for demographic and epidemiological inference with Markov decision processes

inferred← citeshttps://doi.org/10.1093/genetics/iyaf262openalex-snapshot

New methods drive new biology

inferred← citeshttps://doi.org/10.1093/genetics/iyaf263openalex-snapshot

Effects of rescaling forward-in-time population genetic simulations

inferred← citeshttps://doi.org/10.1093/genetics/iyag040openalex-snapshot

Extending the IICR to complex nonstationary structured models

inferred← citeshttps://doi.org/10.1093/genetics/iyag068openalex-snapshot

The illusion of polygenicity in pool-seq genetic mapping studies: insufficient power can mask simple genetic architectures

inferred← citeshttps://doi.org/10.1093/genetics/iyag107openalex-snapshot

Neural posterior estimation for population genetics

inferred← citeshttps://doi.org/10.1093/genetics/iyag132openalex-snapshot

Bursts of reproduction can create genetic structure in frequently recombining bacterial populations

inferred← citeshttps://doi.org/10.1093/gigascience/giac032openalex-snapshot

Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data

inferred← citeshttps://doi.org/10.1093/gigascience/giae021openalex-snapshot

Future-proofing genomic data and consent management: a comprehensive review of technology innovations

inferred← citeshttps://doi.org/10.1093/gigascience/giaf049openalex-snapshot

Analysis-ready VCF at Biobank scale using Zarr

inferred← citeshttps://doi.org/10.1093/gpbjnl/qzaf025openalex-snapshot

LCORL and STC2 Variants Increase Body Size and Growth Rate in Cattle and Other Animals

inferred← citeshttps://doi.org/10.1093/icesjms/fsag130openalex-snapshot

Assessing the potential of runs of homozygosity to infer stock status of commercial bivalves under ongoing anthropogenic disturbances

inferred← citeshttps://doi.org/10.1093/jamiaopen/ooaf107openalex-snapshot

Synthetic data for pharmacogenetics: enabling scalable and secure research

inferred← citeshttps://doi.org/10.1093/molbev/msac212openalex-snapshot

sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S *

inferred← citeshttps://doi.org/10.1093/molbev/msad024openalex-snapshot

Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater BivalveMegalonaias nervosa

inferred← citeshttps://doi.org/10.1093/molbev/msad043openalex-snapshot

Chromosome Fissions and Fusions Act as Barriers to Gene Flow between Brenthis Fritillary Butterflies

inferred← citeshttps://doi.org/10.1093/molbev/msad247openalex-snapshot

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

inferred← citeshttps://doi.org/10.1093/molbev/msad257openalex-snapshot

Inference of Admixture Origins in Indigenous African Cattle

inferred← citeshttps://doi.org/10.1093/molbev/msae077openalex-snapshot

Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning

inferred← citeshttps://doi.org/10.1093/molbev/msae124openalex-snapshot

Rewinding the Ratchet: Rare Recombination Locally Rescues Neo-W Degeneration and Generates Plateaus of Sex-Chromosome Divergence

inferred← citeshttps://doi.org/10.1093/molbev/msae133openalex-snapshot

Exploring the Accuracy and Limits of Algorithms for Localizing Recombination Breakpoints

inferred← citeshttps://doi.org/10.1093/molbev/msae156openalex-snapshot

Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA

inferred← citeshttps://doi.org/10.1093/molbev/msaf002openalex-snapshot

Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences

inferred← citeshttps://doi.org/10.1093/molbev/msaf047openalex-snapshot

K-mer-based Approaches to Bridging Pangenomics and Population Genetics

inferred← citeshttps://doi.org/10.1093/molbev/msaf141openalex-snapshot

Sweeps in Space: Leveraging Geographic Data to Identify Beneficial Alleles in Anopheles gambiae

inferred← citeshttps://doi.org/10.1093/molbev/msaf190openalex-snapshot

The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies

inferred← citeshttps://doi.org/10.1093/molbev/msaf236openalex-snapshot

Accessible, Realistic Genome Simulation with Selection Using stdpopsim

inferred← citeshttps://doi.org/10.1093/molbev/msaf254openalex-snapshot

The Genomic Imprint of Chromosomal Inversions and Demographic History in Island Populations of Deer Mice

inferred← citeshttps://doi.org/10.1093/molbev/msaf257openalex-snapshot

GHIST 2024: The First Genomic History Inference Strategies Tournament

inferred← citeshttps://doi.org/10.1093/molbev/msaf282openalex-snapshot

Efficient Estimation of Nucleotide Diversity and Divergence Using Callable Loci (and More)

inferred← citeshttps://doi.org/10.1093/molbev/msaf283openalex-snapshot

Identifying Single-Origin Rare Variants in Population Genomic Data

inferred← citeshttps://doi.org/10.1093/molbev/msag004openalex-snapshot

Estimating the Reduction in Genetic Diversity from Background Selection under Non-equilibrium Demography and Partial Selfing

inferred← citeshttps://doi.org/10.1093/molbev/msag063openalex-snapshot

Genomic incompatibilities are persistent barriers when speciation happens with gene flow in Formica ants

inferred← citeshttps://doi.org/10.1093/molbev/msag073openalex-snapshot

WASTER: Practical de novo Phylogenomics from Low-coverage Short Reads

inferred← citeshttps://doi.org/10.1093/molbev/msag134openalex-snapshot

Enhancement of hidden Markov model analyses for improved inference of archaic introgression in modern humans

inferred← citeshttps://doi.org/10.1093/molbev/msag136openalex-snapshot

Limited Selection on Neanderthal DNA in 30,780 Recently Admixed Genomes with African-like Ancestry

inferred← citeshttps://doi.org/10.1093/molbev/msag228openalex-snapshot

Characterizing the detectable and invisible fractions of genomic loci under balancing selection

inferred← citeshttps://doi.org/10.1093/molbev/msag237openalex-snapshot

Inferring the demographic history of Chinese and Indian rhesus macaque ( Macaca mulatta ) populations from PacBio HiFi long-read sequencing data

inferred← citeshttps://doi.org/10.1093/nar/gkae1027openalex-snapshot

Deep learning insights into distinct patterns of polygenic adaptation across human populations

inferred← citeshttps://doi.org/10.1093/plcell/koag227openalex-snapshot

Analysis of progenitor genomes offers insights to reduce deleterious burden in hybrid potato breeding

inferred← citeshttps://doi.org/10.1093/sysbio/syad040openalex-snapshot

Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests

inferred← citeshttps://doi.org/10.1093/sysbio/syae028openalex-snapshot

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation

inferred← citeshttps://doi.org/10.1093/sysbio/syae048openalex-snapshot

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models

inferred← citeshttps://doi.org/10.1093/sysbio/syaf059openalex-snapshot

Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent

inferred← citeshttps://doi.org/10.1093/sysbio/syaf081openalex-snapshot

Gene Flow Complicates Phylogenetic Inference in an Archipelago Radiation

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