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@article{tskit2021tskit,
title={Tskit: a portable library for population scale genealogical analysis},
author={{Tskit developers}},
journal={In preparation},
year={2022},
}
@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}
}
@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},
journal = {Nature Genetics},
number = 9,
pages = {1330--1338},
title = {Inferring whole-genome histories in large population datasets},
volume = 51,
year = 2019
}
@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 Genetics},
volume = {7},
pages = {16},
}
@article{kingman1982genealogy,
title={On the genealogy of large populations},
author={Kingman, John F. C.},
journal={Journal of Applied Probability},
volume={19},
number={A},
pages={27--43},
year={1982},
publisher={Cambridge University Press}
}
@article{kingman1982coalescent,
title={The coalescent},
author={Kingman, John F. C.},
journal={Stochastic processes and their applications},
volume={13},
number={3},
pages={235--248},
year={1982},
publisher={Elsevier}
}
@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{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 = {Theoretical Population Biology},
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{wiuf1999recombination,
author ={Carsten Wiuf and Jotun Hein},
title = {Recombination as a Point Process along Sequences},
year = {1999},
journal = {Theoretical Population Biology},
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{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{donnelly1999particle,
title={Particle representations for measure-valued population models},
author={Donnelly, Peter and Kurtz, Thomas G},
journal={Annals of Probability},
volume={27},
number={1},
pages={166--205},
year={1999},
}
@article{donnelly1999genealogical,
title={Genealogical processes for {Fleming}--{Viot} models with selection and recombination},
author={Donnelly, Peter and Kurtz, Thomas G},
journal={Annals of Applied Probability},
volume={9},
number={4},
pages={1091--1148},
year={1999},
}
@article{gonzalezcasanova2018duality,
title={Duality and fixation in {$\Xi$}-{Wright}--{Fisher} processes with frequency-dependent selection},
author={{Gonz\'alez Casanova}, Adri\'an and Span\`o, Dario},
journal={Annals of Applied Probability},
volume={28},
number={1},
pages={250--284},
year={2018},
}
@article{koskela2019robust,
title={Robust model selection between population growth and multiple merger coalescents},
author={Koskela, Jere and {Wilke Berenguer}, Maite},
journal={Mathematical Biosciences},
volume={311},
pages={1--12},
year={2019},
}
@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{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{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{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{nielsen2000estimation,
title={Estimation of population parameters and recombination rates from single nucleotide polymorphisms},
author={Nielsen, Rasmus},
journal={Genetics},
volume={154},
number={2},
pages={931--942},
year={2000},
publisher={Genetics Soc America}
}
@article{wang2008bayesian,
title={Bayesian inference of fine-scale recombination rates using population genomic data},
author={Wang, Ying and Rannala, Bruce},
journal={Philosophical Transactions of the Royal Society B},
volume={363},
pages={3921--3930},
year={2008},
publisher={The Royal Society Publishing}
}
@article{wang2009population,
title={Population genomic inference of recombination rates and hotspots},
author={Wang, Ying and Rannala, Bruce},
journal={Proceedings of the National Academy of Sciences},
volume={106},
number={15},
pages={6215--6219},
year={2009},
publisher={National Acad Sciences}
}
@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{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{heine2018bridging,
title={Bridging trees for posterior inference on ancestral recombination graphs},
author={Heine, Kari and Beskos, Alexandros and Jasra, Ajay and Balding, David and {De Iorio}, Maria},
journal={Proc R Soc A},
volume={474},
pages={20180568},
year={2018},
publisher={The Royal Society Publishing}
}
@article{didelot2010inference,
title={Inference of homologous recombination in bacteria using whole-genome sequences},
author={Didelot, Xavier and Lawson, Daniel and Darling, Aaron and Falush, Daniel},
journal={Genetics},
volume={186},
issue={4},
pages={1435--1449},
year={2010},
publisher={Genetics Soc America}
}
@article{didelot2007inference,
title={Inference of bacterial microevolution using multilocus sequence data},
author={Didelot, Xavier and Falush, Daniel},
journal={Genetics},
volume={175},
issue={3},
pages={1251--1266},
year={2007},
publisher={Genetics Soc America}
}
@article{medina2020speeding,
title={Speeding up Inference of Homologous Recombination in Bacteria},
author={Medina-Aguayo, Felipe J and Didelot, Xavier and Everitt,
Richard G},
journal={bioRxiv},
year={2020},
publisher={Cold Spring Harbor Laboratory}
}
@article{mahmoudi2022bayesian,
author = {Mahmoudi, Ali AND Koskela, Jere AND Kelleher, Jerome AND Chan, Yao-ban AND Balding, David},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Bayesian inference of ancestral recombination graphs},
year = {2022},
month = {03},
volume = {18},
pages = {1-15},
number = {3},
}
@article{zhang2023biobank,
title={Biobank-scale inference of ancestral recombination graphs
enables genealogical analysis of complex traits},
author={Zhang, Brian C and Biddanda, Arjun and Gunnarsson, {\'A}rni
Freyr and Cooper, Fergus and Palamara, Pier Francesco},
journal={Nature Genetics},
pages={768--776},
volume={55},
year={2023},
}
@article{ignatieva2021kwarg,
title={{KwARG}: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation},
author={Ignatieva, Anastasia and Lyngs{\o}, Rune B and Jenkins, Paul A and Hein, Jotun},
journal={Bioinformatics},
volume={37},
issue={19},
pages={3277--3284},
year={2021},
publisher={Oxford University Press}
}
@article{hein1993heuristic,
title={A heuristic method to reconstruct the history of sequences subject to recombination},
author={Hein, Jotun},
journal={Journal of Molecular Evolution},
volume={36},
pages={396--405},
year={1993},
publisher={Springer}
}
@inproceedings{thao2019hybrid,
title={A hybrid approach to optimize the number of recombinations
in ancestral recombination graphs},
author={Thao, Nguyen Thi Phuong and Vinh, Le Sy},
booktitle={Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics},
pages={36--42},
year={2019},
publisher={Association for Computing Machinery}
}
@inproceedings{lyngso2005minimum,
title={Minimum recombination histories by branch and bound},
author={Lyngs{\o}, Rune B and Song, Yun S and Hein, Jotun},
booktitle={International Workshop on Algorithms in Bioinformatics},
pages={239--250},
year={2005},
publisher={Springer}
}
@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{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{mathieson2020ancestry,
title={What is ancestry?},
author={Mathieson, Iain and Scally, Aylwyn},
journal={PLOS Genetics},
volume={16},
number={3},
pages={e1008624},
year={2020},
publisher={Public Library of Science San Francisco, CA USA}
}
@article{ethier1990two,
title={On the two-locus sampling distribution},
author={Ethier, Stewart N and Griffiths, Robert C},
journal={Journal of Mathematical Biology},
volume={29},
number={2},
pages={131--159},
year={1990},
publisher={Springer}
}
@article{mirzaei2017rent,
title={{RENT+}: an improved method for inferring local genealogical trees
from haplotypes with recombination},
author={Mirzaei, Sajad and Wu, Yufeng},
journal={Bioinformatics},
volume={33},
number={7},
pages={1021--1030},
year={2017},
publisher={Oxford University Press}
}
@article{cardona2008extended,
author = {Gabriel Cardona and Francesc Rossell\'o and Gabriel Valiente},
title = {Extended {Newick}: it is time for a standard
representation of phylogenetic networks},
year = {2008},
journal = {BMC Bioinformatics},
volume = {9},
pages = {532},
}
@article{mcgill2013graphml,
title={{GraphML} specializations to codify ancestral recombinant graphs},
author={McGill, James R and Walkup, Elizabeth A and Kuhner, Mary K},
journal={Frontiers in Genetics},
volume={4},
pages = {146},
year={2013},
}
@article{schaefer2021ancestral,
title={An ancestral recombination graph of human, {N}eanderthal, and
{D}enisovan genomes},
author={Schaefer, Nathan K and Shapiro, Beth and Green, Richard E},
journal={Science Advances},
volume={7},
number={29},
pages={eabc0776},
year={2021},
publisher={American Association for the Advancement of
Science}
}
@article{osmond2021estimating,
title={Estimating dispersal rates and locating genetic ancestors with
genome-wide genealogies},
author={Osmond, Matthew and Coop, Graham},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}
@article{grundler2024geographic,
title={A geographic history of human genetic ancestry},
author={Grundler, Michael C and Terhorst, Jonathan and Bradburd, Gideon
S},
journal={bioRxiv},
pages={2024--03},
year={2024},
publisher={Cold Spring Harbor Laboratory}
}
@article{morrison2016genealogies,
title={Genealogies: Pedigrees and phylogenies are reticulating networks not just divergent trees},
author={Morrison, David A},
journal={Evolutionary biology},
volume={43},
number={4},
pages={456--473},
year={2016},
publisher={Springer}
}
@article{krone1997ancestral,
title={Ancestral processes with selection},
author={Krone, Stephen M and Neuhauser, Claudia},
journal={Theoretical Population Biology},
volume={51},
number={3},
pages={210--237},
year={1997},
publisher={Elsevier}
}
@article{neuhauser1997genealogy,
title={The genealogy of samples in models with selection},
author={Neuhauser, Claudia and Krone, Stephen M},
journal={Genetics},
volume={145},
number={2},
pages={519--534},
year={1997},
publisher={Genetics Soc America}
}
@article{neuhauser1999ancestral,
title={The ancestral graph and gene genealogy under frequency-dependent
selection},
author={Neuhauser, Claudia},
journal={Theoretical Population Biology},
volume={56},
number={2},
pages={203--214},
year={1999},
publisher={Elsevier}
}
@article{baumdicker2014infinitely,
title={The infinitely many genes model with horizontal gene transfer},
author={Baumdicker, Franz and Pfaffelhuber, Peter},
journal={Electronic Journal of Probability},
volume={19},
pages={1--27},
year={2014},
publisher={Institute of Mathematical Statistics and Bernoulli
Society}
}
@article{etheridge2009coalescent,
title={A coalescent dual process in a {Moran} model with genic selection},
author={Etheridge, Alison M and Griffiths, Robert C},
journal={Theoretical Population Biology},
volume={75},
number={4},
pages={320--330},
year={2009},
publisher={Elsevier}
}
@article{myers2003bounds,
title={Bounds on the minimum number of recombination events in a sample history},
author={Myers, Simon R and Griffiths, Robert C},
journal={Genetics},
volume={163},
number={1},
pages={375--394},
year={2003},
publisher={Genetics Soc America}
}
@article{song2004minimum,
title={On the minimum number of recombination events in the evolutionary history
of {DNA} sequences},
author={Song, Yun S and Hein, Jotun},
journal={Journal of Mathematical Biology},
volume={48},
number={2},
pages={160--186},
year={2004},
publisher={Springer}
}
@article{song2005constructing,
title={Constructing minimal ancestral recombination graphs},
author={Song, Yun S and Hein, Jotun},
journal={Journal of Computational Biology},
volume={12},
number={2},
pages={147--169},
year={2005},
publisher={Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@article{hein1990reconstructing,
title={Reconstructing evolution of sequences subject to recombination using parsimony},
author={Hein, Jotun},
journal={Mathematical Biosciences},
volume={98},
number={2},
pages={185--200},
year={1990},
publisher={Elsevier}
}
@article{gusfield2007decomposition,
title={A decomposition theory for phylogenetic networks and incompatible characters},
author={Gusfield, Dan and Bansal, Vikas and Bafna, Vineet and Song, Yun S},
journal={Journal of Computational Biology},
volume={14},
number={10},
pages={1247--1272},
year={2007},
publisher={Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@article{gusfield2004optimal,
title={Optimal, efficient reconstruction of phylogenetic networks with constrained recombination},
author={Gusfield, Dan and Eddhu, Satish and Langley, Charles},
journal={Journal of Bioinformatics and Computational Biology},
volume={2},
number={01},
pages={173--213},
year={2004},
publisher={World Scientific}
}
@article{wang2001perfect,
title={Perfect phylogenetic networks with recombination},
author={Wang, Lusheng and Zhang, Kaizhong and Zhang, Louxin},
journal={Journal of Computational Biology},
volume={8},
number={1},
pages={69--78},
year={2001},
publisher={Mary Ann Liebert, Inc.}
}
@article{bordewich2005computational,
title={On the computational complexity of the rooted subtree prune and regraft distance},
author={Bordewich, Magnus and Semple, Charles},
journal={Annals of Combinatorics},
volume={8},
number={4},
pages={409--423},
year={2005},
publisher={Springer}
}
@article{song2005efficient,
title={Efficient computation of close lower and upper bounds on the minimum number of
recombinations in biological sequence evolution},
author={Song, Yun S and Wu, Yufeng and Gusfield, Dan},
journal={Bioinformatics},
volume={21},
number={suppl\_1},
pages={i413--i422},
year={2005},
publisher={Oxford University Press}
}
@article{parida2008estimating,
title={Estimating the ancestral recombinations graph ({ARG}) as compatible
networks of {SNP} patterns},
author={Parida, Laxmi and Mel{\'e}, Marta and Calafell, Francesc and Bertranpetit, Jaume and Genographic Consortium},
journal={Journal of Computational Biology},
volume={15},
number={9},
pages={1133--1153},
year={2008},
publisher={Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@article{parida2011minimal,
title={A minimal descriptor of an ancestral recombinations graph},
author={Parida, Laxmi and Palamara, Pier Francesco and Javed, Asif},
journal={BMC Bioinformatics},
volume={12},
number={1},
pages={1--17},
year={2011},
publisher={BioMed Central}
}
@article{fallon2013acg,
title={{ACG:} rapid inference of population history from recombining nucleotide sequences},
author={O'Fallon, Brendan D},
journal={BMC Bioinformatics},
volume={14},
number={1},
pages={40},
year={2013},
publisher={BioMed Central}
}
@article{griffiths1996ancestral,
title={Ancestral inference from samples of {DNA} sequences with recombination},
author={Griffiths, Robert C and Marjoram, Paul},
journal={Journal of Computational Biology},
volume={3},
number={4},
pages={479--502},
year={1996}
}
@article{fearnhead2001estimating,
title={Estimating recombination rates from population genetic data},
author={Fearnhead, Paul and Donnelly, Peter},
journal={Genetics},
volume={159},
number={3},
pages={1299--1318},
year={2001},
publisher={Genetics Soc America}
}
@article{fearnhead2001perfect,
title={Perfect simulation from population genetic models with selection},
author={Fearnhead, Paul},
journal={Theoretical Population Biology},
volume={59},
number={4},
pages={263--279},
year={2001},
publisher={Elsevier}
}
@article{fearnhead2003ancestral,
title={Ancestral processes for non-neutral models of complex diseases},
author={Fearnhead, Paul},
journal={Theoretical Population Biology},
volume={63},
number={2},
pages={115--130},
year={2003},
publisher={Elsevier}
}
@article{jenkins2011inference,
title={Inference from samples of {DNA} sequences using a two-locus model},
author={Jenkins, Paul A and Griffiths, Robert C},
journal={Journal of Computational Biology},
volume={18},
pages={109--127},
year={2011},
publisher={Mary Ann Liebert}
}
@inproceedings{chan2018likelihood,
title={A likelihood-free inference framework for population genetic data using
exchangeable neural networks},
author={JChan, Jeffrey and Perrone, Valerio and Spence, Jeffrey P and Jenkins,
Paul A and Mathieson, Sara and Song, Yun S},
booktitle={Proceedings of the 32nd International Conference on Neural Information Processing Systems},
pages={8603–8614},
location = {Montr\'{e}al, Canada},
series = {NIPS'18},
year={2018},
publisher = {Curran Associates Inc.}
}
@book{felsenstein2004inferring,
author = {Felsenstein, J.},
publisher = {Sinauer Associates, Inc.},
title = {Inferring phylogenies},
year = {2004}
}
@article{mcvean2002genealogical,
title={A genealogical interpretation of linkage disequilibrium},
author={McVean, Gilean A. T.},
journal={Genetics},
volume={162},
number={2},
pages={987--991},
year={2002},
publisher={Oxford University Press}
}
@article{mcvean2009genealogical,
title={A genealogical interpretation of principal components
analysis},
author={McVean, Gil},
journal={PLOS Genetics},
volume={5},
number={10},
pages={e1000686},
year={2009},
publisher={Public Library of Science San Francisco,
USA}
}
@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{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{camara2016inference,
title={Inference of ancestral recombination graphs through topological
data analysis},
author={C{\'a}mara, Pablo G and Levine, Arnold J and Rabadan, Raul},
journal={PLOS Computational Biology},
volume={12},
number={8},
pages={e1005071},
year={2016},
publisher={Public Library of Science San Francisco, CA USA}
}
@article{wu2011new,
title={New methods for inference of local tree topologies with recombinant
{SNP} sequences in populations},
author={Wu, Yufeng},
journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume={8},
number={1},
pages={182--193},
year={2011},
publisher={IEEE}
}
@article{wu2008association,
title={Association mapping of complex diseases with ancestral recombination graphs:
models and efficient algorithms},
author={Wu, Yufeng},
journal={Journal of Computational Biology},
volume={15},
number={7},
pages={667--684},
year={2008},
publisher={Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}
@inproceedings{song2003parsimonious,
title={Parsimonious reconstruction of sequence evolution and haplotype blocks},
author={Song, Yun S and Hein, Jotun},
booktitle={International Workshop on Algorithms in Bioinformatics},
pages={287--302},
year={2003},
organization={Springer}
}
@article{cardona2008comparison,
title={Comparison of tree-child phylogenetic networks},
author={Cardona, Gabriel and Rossell{\'o}, Francesc and Valiente, Gabriel},
journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume={6},
number={4},
pages={552--569},
year={2008},
publisher={IEEE}
}
@article{choy2005computing,
title={Computing the maximum agreement of phylogenetic networks},
author={Choy, Charles and Jansson, Jesper and Sadakane, Kunihiko and Sung, Wing-Kin},
journal={Theoretical Computer Science},
volume={335},
number={1},
pages={93--107},
year={2005},
publisher={Elsevier}
}
@book{huson2010phylogenetic,
title={Phylogenetic Networks: Concepts, Algorithms and Applications},
author={Huson, Daniel H and Rupp, Regula and Scornavacca, Celine},
year={2010},
publisher={Cambridge University Press}