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@article{gower2021demes,
title={Demes: a standard format for demographic models},
author={Gower, Graham and Ragsdale, Aaron P and others},
journal={In preparation},
year={2021},
}
@article{tskit2021tskit,
title={Tskit: a portable library for population scale genealogical analysis},
author={{Tskit developers}},
journal={In preparation},
year={2021},
}
@article{ragsdale2020lessons,
title={Lessons learned from bugs in models of human history},
author={Ragsdale, Aaron P and Nelson, Dominic and Gravel, Simon and Kelleher, Jerome},
journal={American Journal of Human Genetics},
year={2020},
volume={107},
number={4},
pages={583--588}
}
@article{blum2010abc,
author = {Blum, Michael G.B. and Fran{\c{c}}ois, Olivier},
journal = {Statistics and Computing},
number = {1},
pages = {63--73},
title = {{Non-linear regression models for Approximate Bayesian Computation}},
volume = {20},
year = {2010}
}
@article{raynal2019abc,
author = {Raynal, Louis and Marin, Jean Michel and Pudlo, Pierre and Ribatet, Mathieu
and Robert, Christian P. and Estoup, Arnaud},
journal = {Bioinformatics},
number = {10},
pages = {1720--1728},
title = {{ABC random forests for Bayesian parameter inference}},
volume = {35},
year = {2019}
}
@article{pudlo2016abc,
author = {Pudlo, Pierre and Marin, Jean Michel and Estoup, Arnaud and Cornuet, Jean
Marie and Gautier, Mathieu and Robert, Christian P.},
journal = {Bioinformatics},
number = {6},
pages = {859--866},
title = {{Reliable ABC model choice via random forests}},
volume = {32},
year = {2016}
}
@article{csillery2012abc,
author = {Csill{\'{e}}ry, Katalin and Fran{\c{c}}ois, Olivier and Blum, Michael G B},
journal = {Methods in Ecology and Evolution},
number = {3},
pages = {475--479},
title = {{abc: An R package for approximate Bayesian computation (ABC)}},
volume = {3},
year = {2012}
}
@article{kelleher2016efficient,
title={Efficient coalescent simulation and genealogical analysis for large sample sizes},
author={Kelleher, Jerome and Etheridge, Alison M and McVean, Gilean},
journal={PLoS computational biology},
volume={12},
number={5},
pages={e1004842},
year={2016},
publisher={Public Library of Science}
}
@InCollection{kelleher2020coalescent,
author={Kelleher, Jerome and Lohse, Konrad},
editor={Dutheil, Julien Y.},
title={Coalescent Simulation with msprime},
bookTitle={Statistical Population Genomics},
year={2020},
publisher={Springer US},
address={New York, NY},
pages={191--230},
}
@article{kelleher2018efficient,
author = {Kelleher, Jerome AND Thornton, Kevin R. AND Ashander, Jaime AND
Ralph, Peter L.},
journal = {PLoS Computational Biology},
publisher = {Public Library of Science},
title = {Efficient pedigree recording for fast population genetics simulation},
year = {2018},
month = {11},
volume = {14},
pages = {1-21},
number = {11},
}
@article{haller2018tree,
title={Tree-sequence recording in {SLiM} opens new horizons for
forward-time simulation of whole genomes},
author={Haller, Benjamin C and Galloway, Jared and Kelleher, Jerome and
Messer, Philipp W and Ralph, Peter L},
journal={Molecular ecology resources},
year={2018},
publisher={Wiley Online Library}
}
@article{kelleher2019inferring,
author = {Kelleher, Jerome and Wong, Yan and Wohns, Anthony W. and Fadil, Chaimaa and Albers, Patrick K. and McVean, Gil},
issn = {15461718},
journal = {Nature Genetics},
keywords = {methods tree_sequence tree_sequence_inference},
number = 9,
pages = {1330--1338},
title = {Inferring whole-genome histories in large population datasets},
volume = 51,
year = 2019
}
@article{wohns2021unified,
title={A unified genealogy of modern and ancient genomes},
author={Wohns, Anthony Wilder and Wong, Yan and Jeffery, Ben and
Akbari, Ali and Mallick, Swapan and Pinhasi, Ron and Patterson,
Nick and Reich, David and Kelleher, Jerome and McVean, Gil},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}
@article{mcvean2005approximating,
author ={Gilean A. T. McVean and Niall J. Cardin},
title = {Approximating the coalescent with recombination},
year = {2005},
journal = {Philos Trans R Soc Lond B Biol Sci},
volume = {360},
pages = {1387--1393},
}
@article{marjoram2006fast,
author ={Paul Marjoram and Jeff D Wall},
title = {Fast ``coalescent'' simulation},
year = {2006},
journal = {BMC Genet},
volume = {7},
pages = {16},
}
@article{carvajal2008simulation,
title={Simulation of genomes: a review},
author={Carvajal-Rodr{\'\i}guez, Antonio},
journal={Curr Genomics},
volume={9},
number={3},
pages={155},
year={2008},
}
@article{youfang2008survey,
title={A survey of genetic simulation software for population and epidemiological studies},
author={Liu, Youfang and Athanasiadis, Georgios and Weale, Michael E},
journal={Hum Genomics},
volume={3},
number={1},
pages={79},
year={2008},
}
@article{arenas2012simulation,
title={Simulation of molecular data under diverse evolutionary scenarios},
author={Arenas, Miguel},
journal = {PLoS Comput Biol},
volume={8},
number={5},
pages={e1002495},
year={2012},
}
@article{yuan2012overview,
title={An overview of population genetic data simulation},
author={Yuan, Xiguo and Miller, David J and Zhang, Junying and Herrington, David and Wang, Yue},
journal={J Comput Biol},
volume={19},
number={1},
pages={42--54},
year={2012},
}
@article{hoban2012computer,
title={Computer simulations: tools for population and evolutionary genetics},
author={Hoban, Sean and Bertorelle, Giorgio and Gaggiotti, Oscar E},
journal={Nat Rev Genet},
volume={13},
number={2},
pages={110--122},
year={2012},
}
@article{yang2014critical,
author ={Tao Yang and Hong-Wen Deng and Tianhua Niu},
title = {Critical assessment of coalescent simulators in modeling
recombination hotspots in genomic sequences},
year = {2014},
journal = {BMC Bioinformatics},
volume = {15},
pages = {3},
}
@article{spencer2004selsim,
title={{SelSim:} a program to simulate population genetic
data with natural selection and recombination},
author={Spencer, Chris CA and Coop, Graham},
journal={Bioinformatics},
volume={20},
number={18},
pages={3673--3675},
year={2004},
}
@article{teshima2009mbs,
title={mbs: modifying Hudson's ms software to generate samples of
{DNA} sequences with a biallelic site under selection},
author={Teshima, Kosuke M and Innan, Hideki},
journal={BMC Bioinformatics},
volume={10},
number={1},
pages={166},
year={2009},
}
@article{ewing2010msms,
author ={Gregory Ewing and Joachim Hermisson},
title = {{MSMS:} A Coalescent Simulation Program Including Recombination, Demographic Structure,
and Selection at a Single Locus},
year = {2010},
journal = {Bioinformatics},
volume = {26},
number = {16},
pages = {2064--2065},
}
@article{shlyakhter2014cosi2,
author ={Ilya Shlyakhter and Pardis C. Sabeti and Stephen F. Schaffner},
title = {Cosi2: an efficient simulator of exact and approximate coalescent with selection},
year = {2014},
journal = {Bioinformatics},
volume = {30},
number = {23},
pages = {3427--3429},
}
@article{kingman1982coalescent,
author = {J. F. C. Kingman},
title = {The coalescent},
year = {1982},
journal = {Stoch. Proc. Appl.},
volume = {13},
number = {3},
pages = {235--248},
}
@article {tajima1983evolutionary,
author = {Tajima, Fumio},
title = {Evolutionary relationship of DNA sequences in finite populations},
volume = {105},
number = {2},
pages = {437--460},
year = {1983},
publisher = {Genetics},
issn = {0016-6731},
journal = {Genetics}
}
@article{hudson2002generating,
author ={Richard R. Hudson},
title = {Generating samples under a {Wright-Fisher} neutral model of genetic variation},
year = {2002},
journal = {Bioinformatics},
volume = {18},
number = {2},
pages = {337--338},
}
@article{hudson1990gene,
author = {Richard R. Hudson},
title = {Gene genealogies and the coalescent process},
journal = {Oxford Surveys in Evolutionary Biology},
year = {1990},
volume = {7},
pages = {1-44},
}
@article{hudson1983testing,
title = {Testing the Constant-Rate Neutral Allele Model with Protein Sequence Data},
author = {Richard R. Hudson},
journal = {Evolution},
year = {1983},
volume = {37},
number = {1},
pages = {203--217},
}
@article{hudson1983properties,
title = {Properties of a neutral allele model with intragenic recombination},
author = {Richard R. Hudson},
journal = {Theoretical Population Biology},
year = {1983},
volume = {23},
pages = {183--201},
}
@article{kaplan1985use,
title = {The use of sample genealogies for studying a selectively neutral
$m$-loci model with recombination},
author = {Norman Kaplan and Richard R. Hudson},
journal = {Theor Popul Biol},
year = {1985},
volume = {28},
pages = {382--396},
}
@book{wakely2008coalescent,
author = {Wakeley, John},
title = {Coalescent theory: an introduction},
year = {2008},
address = {Englewood, Colorado},
publisher = {Roberts and Company},
}
@article{griffiths1991two,
title={The two-locus ancestral graph},
author={Griffiths, Robert C},
journal={Lecture Notes-Monograph Series},
volume={18},
pages={100--117},
year={1991},
}
@incollection{griffiths1997ancestral,
author = {Robert C Griffiths and Paul Marjoram},
title = {An ancestral recombination graph},
editor = {Donnelly, P. and Tavar\'e, S.},
booktitle = {Progress in Population Genetics and Human Evolution,
IMA Volumes in Mathematics and its Applications},
volume = {87},
publisher = {Springer-Verlag},
address = {Berlin},
year = {1997},
pages = {257--270},
}
@article{fenwick1994new,
author ={Peter M. Fenwick},
title = {A New Data Structure for Cumulative Frequency Tables},
year = {1994},
journal = {Software: Practice and Experience},
volume = {24},
pages = {327--336},
}
@book{knuth1998sorting,
author = {D. E. Knuth},
title = {Sorting and Searching},
publisher = {Addison-Wesley},
year = {1998},
edition = {Second},
address = {Reading, Massachusetts},
volume = {3 of \emph{The Art of Computer Programming}}}
}
@article{wiuf1999recombination,
author ={Carsten Wiuf and Jotun Hein},
title = {Recombination as a Point Process along Sequences},
year = {1999},
journal = {Theor Popul Biol},
volume = {55},
number = {3},
pages = {248--259},
}
@article{wiuf1999ancestry,
title={The ancestry of a sample of sequences subject to recombination},
author={Wiuf, Carsten and Hein, Jotun},
journal={Genetics},
volume={151},
number={3},
pages={1217--1228},
year={1999},
}
@article{hellenthal2007mshot,
title={msHOT: modifying {Hudson}'s ms simulator to incorporate
crossover and gene conversion hotspots},
author={Hellenthal, Garrett and Stephens, Matthew},
journal={Bioinformatics},
volume={23},
number={4},
pages={520--521},
year={2007}
}
@article{wang2014new,
title={A new method for modeling coalescent processes with recombination},
author={Wang, Ying and Zhou, Ying and Li, Linfeng and Chen,
Xian and Liu, Yuting and Ma, Zhi-Ming and Xu, Shuhua},
journal={BMC Bioinformatics},
volume={15},
number={1},
pages={273},
year={2014},
}
@article{zhu2015hybrid,
title={{Hybrid-Lambda:} simulation of multiple merger and {Kingman}
gene genealogies in species networks and species trees},
author={Zhu, Sha and Degnan, James H and Goldstien, Sharyn J and Eldon, Bjarki},
journal={BMC Bioinformatics},
volume={16},
number={292},
year={2015}
}
@article{schweinsberg2000coalescents,
title={Coalescents with simultaneous multiple collisions},
author={Schweinsberg, Jason},
journal = {Electron J of Probab},
volume={5},
number={12},
pages={1--50},
year={2000},
}
@article{donnelly1999particle,
title={Particle representations for measure-valued population models},
author={Donnelly, Peter and Kurtz, Thomas G},
journal={Ann Probab},
volume={27},
number={1},
pages={166--205},
year={1999},
}
@article{haller2019slim,
title={{SLiM} 3: forward genetic simulations beyond the {Wright--Fisher}
model},
author={Haller, Benjamin C and Messer, Philipp W},
journal={Molecular biology and evolution},
volume={36},
number={3},
pages={632--637},
year={2019},
publisher={Oxford University Press}
}
@article{speidel2019method,
author = {Speidel, Leo and Forest, Marie and Shi, Sinan and Myers, Simon R.},
journal = {Nature Genetics},
number = {9},
pages = {1321--1329},
title = {A method for genome-wide genealogy estimation for thousands of samples},
volume = {51},
year = {2019}
}
@article{harris2019database,
title={From a database of genomes to a forest of evolutionary trees},
author={Harris, Kelley},
journal={Nature genetics},
volume={51},
number={9},
pages={1306--1307},
year={2019},
publisher={Nature Publishing Group}
}
@article{tang2019genealogy,
title={Genealogy at the genome scale},
author={Tang, Lin},
journal={Nature methods},
volume={16},
number={11},
pages={1077--1077},
year={2019},
}
@article{adrion2020community,
title={A community-maintained standard library of population genetic
models},
author={Adrion, Jeffrey R and Cole, Christopher B and Dukler, Noah and
Galloway, Jared G and Gladstein, Ariella L and Gower, Graham and
Kyriazis, Christopher C and Ragsdale, Aaron P and Tsambos,
Georgia and Baumdicker, Franz and others},
journal={Elife},
volume={9},
pages={e54967},
year={2020},
publisher={eLife Sciences Publications Limited}
}
@article{kern2016discoal,
title={Discoal: flexible coalescent simulations with selection},
author={Kern, Andrew D and Schrider, Daniel R},
journal={Bioinformatics},
volume={32},
number={24},
pages={3839--3841},
year={2016},
publisher={Oxford University Press}
}
@article{wilton2015smc,
title={The SMC' is a highly accurate approximation to the ancestral
recombination graph},
author={Wilton, Peter R and Carmi, Shai and Hobolth, Asger},
journal={Genetics},
volume={200},
number={1},
pages={343--355},
year={2015},
publisher={Genetics Soc America}
}
@article{bhaskar2014distortion,
title={Distortion of genealogical properties when the sample is very
large},
author={Bhaskar, Anand and Clark, Andrew G and Song, Yun S},
journal={Proceedings of the National Academy of Sciences},
volume={111},
number={6},
pages={2385--2390},
year={2014},
publisher={National Acad Sciences}
}
@article{palamara2016argon,
title={ARGON: fast, whole-genome simulation of the discrete time
Wright-fisher process},
author={Palamara, Pier Francesco},
journal={Bioinformatics},
volume={32},
number={19},
pages={3032--3034},
year={2016},
publisher={Oxford University Press}
}
@article{wakeley2012gene,
title={Gene genealogies within a fixed pedigree, and the robustness of
Kingman’s coalescent},
author={Wakeley, John and King, L{\'e}andra and Low, Bobbi S and
Ramachandran, Sohini},
journal={Genetics},
volume={190},
number={4},
pages={1433--1445},
year={2012},
publisher={Genetics Soc America}
}
@article{nelson2020accounting,
author = {Dominic Nelson and Jerome Kelleher and Aaron P. Ragsdale and
Claudia Moreau and Gil McVean and Simon Gravel},
journal = {PLoS Genetics},
publisher = {Public Library of Science},
title = {Accounting for long-range correlations in genome-wide
simulations of large cohorts},
year = {2020},
pages = {In press},
}
@article{peischl2013sequential,
title={A sequential coalescent algorithm for chromosomal inversions},
author={Peischl, S and Koch, E and Guerrero, RF and Kirkpatrick, M},
journal={Heredity},
volume={111},
pages={200--209},
year={2013},
}
@article{eriksson2009sequential,
title={Sequential {Markov} coalescent algorithms for population models with
demographic structure},
author={Eriksson, Anders and Mahjani, B and Mehlig, Bernhard},
journal = {Theoretical Population Biology},
volume={76},
number={2},
pages={84--91},
year={2009},
}
@article{arenas2010coalescent,
title={Coalescent simulation of intracodon recombination},
author={Arenas, Miguel and Posada, David},
journal={Genetics},
volume={184},
number={2},
pages={429--437},
year={2010},
}
@article{wiuf2000coalescent,
title={The coalescent with gene conversion},
author={Wiuf, Carsten and Hein, Jotun},
journal={Genetics},
volume={155},
number={1},
pages={451--462},
year={2000},
publisher={Genetics Soc America}
}
@article{heled2009bayesian,
title={Bayesian inference of species trees from multilocus data},
author={Heled, Joseph and Drummond, Alexei J},
journal={Molecular biology and evolution},
volume={27},
number={3},
pages={570--580},
year={2009},
publisher={Society for Molecular Biology and Evolution}
}
@article{kuhner2000maximum,
title={Maximum likelihood estimation of recombination rates from
population data},
author={Kuhner, Mary K and Yamato, Jon and Felsenstein, Joseph},
journal={Genetics},
volume={156},
number={3},
pages={1393--1401},
year={2000},
publisher={Genetics Soc America}
}
@article{cartwright2005dna,
title={{DNA} assembly with gaps ({Dawg}): simulating sequence evolution},
author={Cartwright, Reed A},
journal={Bioinformatics},
volume={21},
number={Suppl\_3},
pages={iii31--iii38},
year={2005},
publisher={Oxford University Press}
}
@article{rambaut1997seq,
title={{Seq-Gen}: an application for the Monte Carlo simulation of DNA
sequence evolution along phylogenetic trees},
author={Rambaut, Andrew and Grassly, Nicholas C},
journal={Bioinformatics},
volume={13},
number={3},
pages={235--238},
year={1997},
publisher={Oxford University Press}
}
@article{minichiello2006mapping,
title={Mapping trait loci by use of inferred ancestral recombination
graphs},
author={Minichiello, Mark J and Durbin, Richard},
journal={The American Journal of Human Genetics},
volume={79},
number={5},
pages={910--922},
year={2006},
publisher={Elsevier}
}
@article{rasmussen2014genome,
title={Genome-wide inference of ancestral recombination graphs},
author={Rasmussen, Matthew D and Hubisz, Melissa J and Gronau, Ilan and
Siepel, Adam},
journal={PLoS genetics},
volume={10},
number={5},
pages={e1004342},
year={2014},
publisher={Public Library of Science}
}
@article{becheler2020occupancy,
author = {Becheler, Arnaud and Knowles, L Lacey},
title = {Occupancy spectrum distribution: application for coalescence
simulation with generic mergers},
journal = {Bioinformatics},
year = {2020},
month = {02},
issn = {1367-4803},
note = {btaa090},
}
@article{becheler2019quetzal,
title={The Quetzal Coalescence template library: A {C++} programmers
resource for integrating distributional, demographic and coalescent
models},
author={Becheler, Arnaud and Coron, Camille and Dupas, St{\'e}phane},
journal={Molecular ecology resources},
volume={19},
number={3},
pages={788--793},
year={2019},
publisher={Wiley Online Library}
}
@article{thornton2014cpp,
title={A {C++} template library for efficient forward-time population
genetic simulation of large populations},
author={Thornton, Kevin R},
journal={Genetics},
volume={198},
number={1},
pages={157--166},
year={2014},
publisher={Genetics Soc America}
}
@article{li2011inference,
author ={Heng Li and Richard Durbin},
title = {Inference of human population history from individual whole-genome sequences},
year = {2011},
journal = {Nature},
volume = {475},
pages = {493--496},
}
@article{schiffels2014inferring,
author ={Stephan Schiffels and Richard Durbin},
title = {Inferring human population size and separation history from multiple genome sequences},
year = {2014},
journal= {Nat Genet},
volume = {46},
pages = {919--925},
}
@article{harris2013inferring,
title={Inferring demographic history from a spectrum of shared haplotype lengths},
author={Harris, Kelley and Nielsen, Rasmus},
journal={PLoS genetics},
volume={9},
number={6},
pages={e1003521},
year={2013},
publisher={Public Library of Science}
}
@article{nielsen2000estimation,
title={Estimation of population parameters and recombination rates from single nucleotide
polymorphism},
author={Nielsen, Rasmus},
journal={Genetics},
volume={154},
number={2},
pages={931--942},
year={2000},
publisher={Genetics Soc America}
}
@article{wang2008bayesian,
author = {Wang, Ying and Rannala, Bruce},
title = {Bayesian inference of fine-scale recombination rates using population genomic data},
journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
volume = {363},
number = {1512},
pages = {3921--3930},
year = {2008}
}
@article{carmi2014renewal,
title={A renewal theory approach to {IBD} sharing},
author={Carmi, Shai and Wilton, Peter R and Wakeley, John and Pe'er, Itsik},
journal={Theoretical population biology},
volume={97},
pages={35--48},
year={2014},
publisher={Elsevier}
}
@article{zheng2014bayesian,
title={Bayesian inference of local trees along chromosomes by the sequential Markov coalescent},
author={Zheng, Chaozhi and Kuhner, Mary K and Thompson, Elizabeth A},
journal={Journal of molecular evolution},
volume={78},
number={5},
pages={279--292},
year={2014},
publisher={Springer}
}
@article{sheehan2013estimating,
title={Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach},
author={Sheehan, Sara and Harris, Kelley and Song, Yun S},
journal={Genetics},
volume={194},
number={3},
pages={647--662},
year={2013},
publisher={Genetics Soc America}
}
@article{terhorst2017robust,
title={Robust and scalable inference of population history from hundreds of unphased whole genomes},
author={Terhorst, Jonathan and Kamm, John A and Song, Yun S},
journal={Nature genetics},
volume={49},
number={2},
pages={303--309},
year={2017},
publisher={Nature Research}
}
@article{hobolth2014markovian,
title={Markovian approximation to the finite loci coalescent with recombination along multiple sequences},
author={Hobolth, Asger and Jensen, Jens Ledet},
journal={Theoretical population biology},
volume={98},
pages={48--58},
year={2014},
publisher={Elsevier}
}
@article{liu2008survey,
title={A survey of genetic simulation software for population and
epidemiological studies},
author={Liu, Youfang and Athanasiadis, Georgios and Weale, Michael E},
journal={Human genomics},
volume={3},
number={1},
pages={79},
year={2008},
publisher={BioMed Central}
}
@article{martin2017human,
title={Human demographic history impacts genetic risk prediction across diverse populations},
author={Martin, Alicia R and Gignoux, Christopher R and Walters, Raymond K and Wojcik, Genevieve L
and Neale, Benjamin M and Gravel, Simon and Daly, Mark J and Bustamante, Carlos D and Kenny, Eimear E},
journal={The American Journal of Human Genetics},
volume={100},
number={4},
pages={635--649},
year={2017},
publisher={Elsevier}
}
@article{martin2020erratum,
title={Erratum: Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations (The American Journal of Human Genetics (2020) 107 (4)(583--588),(S000292972030286X),(10.1016/j. ajhg. 2020.08. 017))},
author={Martin, Alicia R and Gignoux, Christopher R and Walters, Raymond K
and Wojcik, Genevieve L and Neale, Benjamin M and Gravel, Simon
and Daly, Mark J and Bustamante, Carlos D and Kenny, Eimear E},
journal={American journal of human genetics},
volume={107},
number={4},
pages={788--789},
year={2020},
publisher={Cell Press}
}
@article{staab2015scrm,
title={scrm: Efficiently simulating long sequences using the approximated
coalescent with recombination},
author={Staab, Paul R and Zhu, Sha and Metzler, Dirk and Lunter,
Gerton},
journal={Bioinformatics},
volume={31},
number={10},
pages={1680--1682},
year={2015},
publisher={Oxford University Press}
}
@book{hein2004gene,
title={Gene genealogies, variation and evolution: a primer in coalescent
theory},
author={Hein, Jotun and Schierup, Mikkel and Wiuf, Carsten},
year={2004},
publisher={Oxford University Press, USA}
}
@article{stephens2015big,
title={Big data: astronomical or genomical?},
author={Stephens, Zachary D and Lee, Skylar Y and Faghri, Faraz and
Campbell, Roy H and Zhai, Chengxiang and Efron, Miles J and Iyer,
Ravishankar and Schatz, Michael C and Sinha, Saurabh and Robinson,
Gene E},
journal={PLoS biology},
volume={13},
number={7},
pages={e1002195},
year={2015},
publisher={Public Library of Science}
}
@article{bycroft2018genome,
title={The {UK} {Biobank} resource with deep phenotyping and genomic data},
author={Bycroft, Clare Freeman, Colin and Petkova, Desislava and
Band, Gavin and Elliott, Lloyd T and Sharp, Kevin and Motyer, Allan
and Vukcevic, Damjan and Delaneau, Olivier and O'Connell, Jared
and others},
journal={Nature},
volume={562},
pages={203–209},
year={2018},
}
@article{felsenstein1989phylip,
author ={Joseph Felsenstein},
title = {{PHYLIP}---phylogeny inference package (version 3.2)},
year = {1989},
journal = {Cladistics},
volume = {5},
pages = {164--166},
}
@article{ralph2020efficiently,
title={Efficiently summarizing relationships in large samples: a general
duality between statistics of genealogies and genomes},
author={Ralph, Peter and Thornton, Kevin and Kelleher, Jerome},
journal={Genetics},
volume={215},
number={3},
pages={779--797},
year={2020},
publisher={Oxford University Press}
}
@article{baumdicker2014AGTG,
author = {Baumdicker, Franz and Pfaffelhuber, Peter},
doi = {10.1214/EJP.v19-2642},
journal = {Electronic Journal of Probability},
keywords = {Prokaryote,bacterial evolution,coalescent,gene frequency spectrum,pangenome},
pages = {1--27},
title = {{The infinitely many genes model with horizontal gene transfer}},
volume = {19},
year = {2014}
}
@article{brown2016simbac,
author = {Brown, Thomas and Didelot, Xavier and Wilson, Daniel J. and Maio, Nicola De},
journal = {Microbial Genomics},
number = {1},
pages = {1--6},
pmid = {27713837},
title = {{SimBac: simulation of whole bacterial genomes with homologous recombination}},
volume = {2},
year = {2016}
}
@article{spielman2015pyvolve,
title={Pyvolve: a flexible Python module for simulating sequences along phylogenies},
author={Spielman, Stephanie J and Wilke, Claus O},
journal={PloS one},
volume={10},
number={9},
year={2015},
publisher={Public Library of Science}
}
@article{wang2020tracking,
title={Tracking human population structure through time from whole genome sequences},
author={Wang, Ke and Mathieson, Iain and O'Connell, Jared and Schiffels, Stephan},
journal={PLoS Genetics},
volume={16},
number={3},
pages={e1008552},
year={2020},
publisher={Public Library of Science}
}
@article{griffiths1994sampling,
author = {Griffiths, R. C. and Tavare, Simon and Bodmer, Walter Fred and Donnelly, Peter James },
title = {Sampling theory for neutral alleles in a varying environment},
journal = {Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences},
volume = {344},
number = {1310},
pages = {403-410},
year = {1994},
doi = {10.1098/rstb.1994.0079},
}
@article{keightley2007joint,
author = {Keightley, Peter D. and Eyre-Walker, Adam},
title = {Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies},
volume = {177},
number = {4},
pages = {2251--2261},
year = {2007},
doi = {10.1534/genetics.107.080663},
publisher = {Genetics},
issn = {0016-6731},
journal = {Genetics}
}
@article{galtier2000detecting,
Author = {Galtier, Nicolas and Depaulis, Frantz and Barton, N. H.},
Journal = {Genetics},