This repository has been archived by the owner on Aug 24, 2022. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 21
/
paper.bib
2510 lines (2280 loc) · 74.3 KB
/
paper.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@misc{condaforge2015,
author= {conda-forge community},
title = {{The conda-forge Project: Community-based Software
Distribution Built on the conda Package Format
and Ecosystem}},
month = jul,
year = 2015,
publisher = {Zenodo},
doi = {10.5281/zenodo.4774216},
url = {https://doi.org/10.5281/zenodo.4774216}
}
@article{vendrami2021sweepstake,
title={Sweepstake reproductive success and collective dispersal produce
chaotic genetic patchiness in a broadcast spawner},
author={Vendrami, David LJ and Peck, Lloyd S and Clark, Melody S and
Eldon, Bjarki and Meredith, Michael and Hoffman, Joseph I},
journal={Science advances},
volume={7},
number={37},
pages={eabj4713},
year={2021},
publisher={American Association for the Advancement of Science}
}
@article{johri2021statistical,
title={Statistical inference in population genomics},
author={Johri, P and Aquadro, CF and Beaumont, M and Charlesworth, B
and Excoffier, L and Eyre-Walker, A and Keightley, PD and Lynch, M
and McVean, G and Payseur, BA and others},
year={2021}
}
@article{charlesworth2021effects,
title={Effects of Selection at Linked Sites on Patterns of Genetic
Variability},
author={Charlesworth, Brian and Jensen, Jeffrey D},
journal={Annual Review of Ecology, Evolution, and Systematics},
volume={52},
pages={177--197},
year={2021},
publisher={Annual Reviews}
}
@article{charlesworth1993effect,
title={The effect of deleterious mutations on neutral molecular
variation},
author={Charlesworth, Brian and Morgan, MT and Charlesworth, Deborah},
journal={Genetics},
volume={134},
number={4},
pages={1289--1303},
year={1993},
publisher={Genetics Soc America}
}
@article{charlesworth1995pattern,
title={The pattern of neutral molecular variation under the background
selection model},
author={Charlesworth, Deborah and Charlesworth, Brian and Morgan, MT},
journal={Genetics},
volume={141},
number={4},
pages={1619--1632},
year={1995},
publisher={Genetics Soc America}
}
@article{comeron2014background,
title={Background selection as baseline for nucleotide variation across
the {Drosophila} genome},
author={Comeron, Josep M},
journal={PLoS Genetics},
volume={10},
number={6},
pages={e1004434},
year={2014},
publisher={Public Library of Science San Francisco, USA}
}
@conference{kluyver2016jupyter,
Title = {Jupyter Notebooks -- a publishing format for reproducible
computational workflows},
Author = {Thomas Kluyver and Benjamin Ragan-Kelley and Fernando P{\'e}rez
and Brian Granger and Matthias Bussonnier and Jonathan Frederic and
Kyle Kelley and Jessica Hamrick and Jason Grout and Sylvain Corlay
and Paul Ivanov and Dami{\'a}n Avila and Safia Abdalla and Carol
Willing},
Booktitle = {Positioning and Power in Academic Publishing: Players, Agents
and Agendas},
Editor = {F. Loizides and B. Schmidt},
Organization = {IOS Press},
Pages = {87 - 90},
Year = {2016}
}
@article{shannon2019gender,
title={Gender equality in science, medicine, and global health: where are
we at and why does it matter?},
author={Shannon, Geordan and Jansen, Melanie and Williams, Kate and
C{\'a}ceres, Carlos and Motta, Angelica and Odhiambo, Aloyce and
Eleveld, Alie and Mannell, Jenevieve},
journal={The Lancet},
volume={393},
number={10171},
pages={560--569},
year={2019},
publisher={Elsevier}
}
@article{dung2019illuminating,
title={Illuminating women’s hidden contribution to historical theoretical
population genetics},
author={Dung, Samantha Kristin and L{\'o}pez, Andrea and Barragan,
Ezequiel Lopez and Reyes, Rochelle-Jan and Thu, Ricky and
Castellanos, Edgar and Catalan, Francisca and
Huerta-S{\'a}nchez, Emilia and Rohlfs, Rori V},
journal={Genetics},
volume={211},
number={2},
pages={363--366},
year={2019},
publisher={Oxford University Press}
}
@article{wellenreuther2016women,
title={Women in evolution--highlighting the changing face of evolutionary
biology},
author={Wellenreuther, Maren and Otto, Sarah},
journal={Evolutionary Applications},
volume={9},
number={1},
pages={3--16},
year={2016},
publisher={Wiley Online Library}
}
@article{bonham2017women,
title={Women are underrepresented in computational biology: An analysis
of the scholarly literature in biology, computer science and
computational biology},
author={Bonham, Kevin S and Stefan, Melanie I},
journal={PLoS computational biology},
volume={13},
number={10},
pages={e1005134},
year={2017},
publisher={Public Library of Science San Francisco, CA USA}
}
@article{trinkenreich2021women,
title={Women's Participation in Open Source Software: A Survey of the
Literature},
author={Trinkenreich, Bianca and Wiese, Igor and Sarma, Anita and
Gerosa, Marco and Steinmacher, Igor},
journal={arXiv preprint arXiv:2105.08777},
year={2021}
}
@article{miga2020telomere,
title={Telomere-to-telomere assembly of a complete human {X} chromosome},
author={Miga, Karen H and Koren, Sergey and Rhie, Arang and Vollger,
Mitchell R and Gershman, Ariel and Bzikadze, Andrey and Brooks,
Shelise and Howe, Edmund and Porubsky, David and Logsdon, Glennis A
and others},
journal={Nature},
volume={585},
number={7823},
pages={79--84},
year={2020},
publisher={Nature Publishing Group}
}
@article{gardner2021sustained,
title={Sustained software development, not number of citations or journal
choice, is indicative of accurate bioinformatic software},
author={Gardner, Paul P and Paterson, James M and McGimpsey, Stephanie
R and Ghomi, Fatemeh Ashari and Umu, Sinan U and Pawlik, Aleksandra
and Gavryushkin, Alex and Black, Michael A},
journal={bioRxiv},
pages={092205},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}
@article{harris2020array,
title={Array programming with NumPy},
author={Harris, Charles R and Millman, K Jarrod and van der Walt,
St{\'e}fan J and Gommers, Ralf and Virtanen, Pauli and Cournapeau,
David and Wieser, Eric and Taylor, Julian and Berg, Sebastian and
Smith, Nathaniel J and others},
journal={Nature},
volume={585},
number={7825},
pages={357--362},
year={2020},
publisher={Nature Publishing Group}
}
@article{neher2013genealogies,
title={Genealogies of rapidly adapting populations},
author={Neher, Richard A and Hallatschek, Oskar},
journal={Proceedings of the National Academy of Sciences},
volume={110},
number={2},
pages={437--442},
year={2013},
publisher={National Acad Sciences}
}
@article{desai2013genetic,
title={Genetic diversity and the structure of genealogies in rapidly
adapting populations},
author={Desai, Michael M and Walczak, Aleksandra M and Fisher, Daniel
S},
journal={Genetics},
volume={193},
number={2},
pages={565--585},
year={2013},
publisher={Oxford University Press}
}
@article{schweinsberg2017rigorous,
title={Rigorous results for a population model with selection {II}:
genealogy of the population},
author={Schweinsberg, Jason},
journal={Electronic Journal of Probability},
volume={22},
pages={1--54},
year={2017},
publisher={Institute of Mathematical Statistics and Bernoulli
Society}
}
@article {gaynor2021alphasimr,
author = {Gaynor, R. Chris and Gorjanc, Gregor and Hickey, John M.},
title = {{AlphaSimR}: An {R}-package for Breeding Program Simulations},
volume = {11},
year = {2021},
doi = {10.1093/g3journal/jkaa017},
journal = {G3: Genes, Genomes, Genetics}
}
@article{jouganous2017inferring,
title={Inferring the joint demographic history of multiple populations:
beyond the diffusion approximation},
author={Jouganous, Julien and Long, Will and Ragsdale, Aaron P and Gravel, Simon},
journal={Genetics},
volume={206},
number={3},
pages={1549--1567},
year={2017},
publisher={Oxford University Press}
}
@article{gower2021demes,
title={Demes: a standard format for demographic models},
author={Gower, Graham and Ragsdale, Aaron P and others},
journal={In preparation},
year={2022},
}
@article{tskit2021tskit,
title={Tskit: a portable library for population scale genealogical analysis},
author={{Tskit developers}},
journal={In preparation},
year={2022},
}
@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 {B}ayesian 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},
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 Computational Biology},
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={Journal of Computational Biology},
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={Nature Reviews Genetics},
volume={13},
number={2},
pages={110--122},
year={2012},
publisher={Nature Publishing Group}
}
@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 {H}udson'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{kingman1982genealogy,
title={On the genealogy of large populations},
author={Kingman, John FC},
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{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 = {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{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 = {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{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
{W}right-{F}isher 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,
title={Accounting for long-range correlations in genome-wide simulations
of large cohorts},
author={Nelson, Dominic and Kelleher, Jerome and Ragsdale, Aaron P and
Moreau, Claudia and McVean, Gil and Gravel, Simon},
journal={PLoS genetics},
volume={16},
number={5},
pages={e1008619},
year={2020},
publisher={Public Library of Science San Francisco, CA USA}
}
@article{peischl2013sequential,
title={A sequential coalescent algorithm for chromosomal inversions},
author={Peischl, Stephan and Koch, E and Guerrero, RF and Kirkpatrick, Mark},
journal={Heredity},
volume={111},
number={3},
pages={200--209},
year={2013},
publisher={Nature Publishing Group}
}
@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 {M}onte {C}arlo 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},