81. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, Depristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011; 27: 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 PMID: 21653522

82. Weir BS, Cockerham CC. Estimating F-Statistics for the Analysis of Population Structure. Evolution (N Y). 1984; 38: 1358–1370. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x PMID: 28563791

83. Lu S, Platz GJ, Edwards MC, Friesen TL. Mating type locus-specific polymerase chain reaction markers for differentiation of Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of barley net blotch. Phytopathology. 2010; 100: 1298–1306. https://doi.org/10.1094/PHYTO-05-10-0135 PMID: 20731534

84. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: Architecture and applications. BMC Bioinformatics. 2009; 10: 1–9. https://doi.org/10.1186/1471-2105-10-421 PMID: 20003500

85. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013; 30: 772–780. https://doi.org/10.1093/molbev/mst010 PMID: 23329690

86. Okonechnikov K, Golosova O, Fursov M, Varlamov A, Vaskin Y, Efremov I, et al. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics. 2012; 28: 1166–1167. https://doi.org/10.1093/bioinformatics/bts091 PMID: 22368248

87. Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016; 11: 1–10. https://doi.org/10.1371/journal.pone.0163962 PMID: 27706213

88. Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32: 268–274. https://doi.org/10.1093/molbev/msu300 PMID: 25371430

89. Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat Methods. 2017; 14: 587–589. https://doi.org/10.1038/nmeth.4285 PMID: 28481363

90. Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the ultrafast boot-strap approximation. Mol Biol Evol. 2018; 35: 518–522. https://doi.org/10.1093/molbev/msx281 PMID: 29077904

91. Hoang DT, Vinh LS, Flouri T, Stamatakis A, Von Haeseler A, Minh BQ. MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol Biol. 2018; 18: 1–11. https://doi.org/10.1186/s12862-018-1131-3 PMID: 29390973

92. Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C. Reversible polymorphism-aware phylogenetic models and their application to tree inference. J Theor Biol. 2016; 407: 362–370. https://doi.org/10.1016/j.jtbi.2016.07.042 PMID: 27480613

93. Hudson RR. Generating samples under a Wright–Fisher neutral model ofgenetic variation. Bioinformatics. 2002; 18: 337–338. https://doi.org/10.1093/bioinformatics/18.2.337 PMID: 11847089

94. Kim Y, Neilsen R. Linkage disequilibrium as a signature of selective sweeps. Genetics. 2004; 167: 1513–1524. https://doi.org/10.1534/genetics.103.025387 PMID: 15280259

95. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Res. 2005; 15: 1566–1575. https://doi.org/10.1101/gr.4252305 PMID: 16251466

96. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: An information aesthetic for comparative genomics. Genome Res. 2009; 19: 1639–1645. https://doi.org/10.1101/gr.092759.109 PMID: 19541911

97. Clare SJ, Wyatt NA, Brueggeman RS, Friesen TL. Research advances in the Pyrenophora teres–barley interaction. Mol Plant Pathol. 2020; 21: 272–288. https://doi.org/10.1111/mpp.12896 PMID: 31837102

98. Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26: 841–842. https://doi.org/10.1093/bioinformatics/btq033 PMID: 20110278
81. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, Depristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011; 27: 2156–2158. https://doi.org/10.1093/bioinformatics/btr330 PMID: 21653522

82. Weir BS, Cockerham CC. Estimating F-Statistics for the Analysis of Population Structure. Evolution (N Y). 1984; 38: 1358–1370. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x PMID: 28563791

83. Lu S, Platz GJ, Edwards MC, Friesen TL. Mating type locus-specific polymerase chain reaction markers for differentiation of Pyrenophora teres f. teres and P. teres f. maculata, the causal agents of barley net blotch. Phytopathology. 2010; 100: 1298–1306. https://doi.org/10.1094/PHYTO-05-10-0135 PMID: 20731534

84. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: Architecture and applications. BMC Bioinformatics. 2009; 10: 1–9. https://doi.org/10.1186/1471-2105-10-421 PMID: 20003500

85. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013; 30: 772–780. https://doi.org/10.1093/molbev/mst010 PMID: 23329690

86. Okonechnikov K, Golosova O, Fursov M, Varlamov A, Vaskin Y, Efremov I, et al. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics. 2012; 28: 1166–1167. https://doi.org/10.1093/bioinformatics/bts091 PMID: 22368248

87. Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016; 11: e106392 PMID: 27706213

88. Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015; 32: 268–274. https://doi.org/10.1093/molbev/msu300 PMID: 25371430

89. Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat Methods. 2017; 14: 587–589. https://doi.org/10.1038/nmeth.4285 PMID: 28481363

90. Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the ultrafast boot-strap approximation. Mol Biol Evol. 2018; 35: 518–522. https://doi.org/10.1093/molbev/msx281 PMID: 29077904

91. Hoang DT, Vinh LS, Flouri T, Stamatakis A, Von Haeseler A, Minh BQ. MPBoot: Fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol Biol. 2018; 18: 1–11. https://doi.org/10.1186/s12862-018-1131-3 PMID: 29390973

92. Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C. Reversible polymorphism-aware phylogenetic models and their application to tree inference. J Theor Biol. 2016; 407: 362–370. https://doi.org/10.1016/j.jtbi.2016.07.042 PMID: 27480613

93. Hudson RR. Generating samples under a Wright–Fisher neutral model ofgenetic variation. Bioinformatics. 2002; 18: 337–338. https://doi.org/10.1093/bioinformatics/18.2.337 PMID: 11847089

94. Kim Y, Neilsen R. Linkage disequilibrium as a signature of selective sweeps. Genetics. 2004; 167: 1513–1524. https://doi.org/10.1534/genetics.103.025387 PMID: 15280259

95. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Res. 2005; 15: 1566–1575. https://doi.org/10.1101/gr.4252305 PMID: 16251466

96. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: An information aesthetic for comparative genomics. Genome Res. 2009; 19: 1639–1645. https://doi.org/10.1101/gr.092759.109 PMID: 19541911

97. Clare SJ, Wyatt NA, Brueggeman RS, Friesen TL. Research advances in the Pyrenophora teres–barley interaction. Mol Plant Pathol. 2020; 21: 272–288. https://doi.org/10.1111/mpp.12896 PMID: 31837102

98. Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26: 841–842. https://doi.org/10.1093/bioinformatics/btq033 PMID: 20110278