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68. Saujet L, Pereira FC, Henriques AO, Martin-Verstraete I. The regulatory network controlling spore formation in *Clostridium difficile*. FEMS Microbiol Lett. 2014 Sep; 358(1):1–10.

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70. Marteyn B, Scorza FB, Sansonetti PJ, Tang C. Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract. Cell Microbiol. 2011; 13(2):171–6. https://doi.org/10.1111/j.1462-5822.2010.01549.x PMID: 21166974

71. Fimlaid KA, Bond JP, Schutz KC, Putnam EE, Leung JM, Lawley TD, et al. Global Analysis of the Sporulation Pathway of Clostridium difficile. PLoS Genet. 2013 Aug 8; 9(8):e1003660.

72. Garcia-Garcia T, Douché T, Gianetto QG, Poncet S, El Omrani N, Smits WK, et al. In-depth characterization of the Clostridioides difficile phosphoproteome to identify Ser/Thr kinase substrates. Mol Cell Proteomics. 2022 Oct; 10(428). https://doi.org/10.1016/j.mcpro.2022.100428 PMID: 36252736

73. McBride S. Glycine fermentation by C. difficile promotes virulence, spore formation, and is induced by host cathelicidin.

74. Andreesen JR. Glycine metabolism in anaerobes. Antonie Van Leeuwenhoek. 1994; 66(1–3):223–37. https://doi.org/10.1007/BF00871641 PMID: 7747933
54. Monot M, Eckert C, Lemire A, Hamiot A, Dubois T, Tessier C, et al. Clostridium difficile: New Insights into the Evolution of the Pathogenicity Locus. Sci Rep. 2015 Oct 8; 5:15023. https://doi.org/10.1038/srep15023 PMID: 26446480

55. Boratyn GM, Thierry-Mieg J, Thierry-Mieg D, Busby B, Madden TL. Magic-BLAST, an accurate RNA-seq aligner for long and short reads. BMC Bioinformatics. 2019 Jul 25; 20(1):405. https://doi.org/10.1186/s12859-019-2996-x PMID: 31345161

56. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021 Jul 2; 49(W1):W293–6.

57. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, et al. MicroScope: a platform for microbial genome annotation and comparative genomics. Database J Biol Databases Curation. 2009;2009:bap021.

58. Kurka H, Ehrenreich A, Ludwig W, Monot M, Rupnik M, Barbut F, et al. Sequence Similarity of Clostridium difficile Strains by Analysis of Conserved Genes and Genome Content Is Reflected by Their Ribotype Affiliation. PLoS ONE. 2014 Jan 23; 9(1):e86535. https://doi.org/10.1371/journal.pone.0086535 PMID: 24482682

59. Sorg JA, Sonenshein AL. Bile Salts and Glycine as Cogerminants for Clostridium difficile Spores. J Bacteriol. 2008 Apr; 190(7):2505–12. https://doi.org/10.1128/JB.01765-07 PMID: 18245298

60. Theriot CM, Bowman AA, Young VB. Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine. mSphere. 2016 Jan 6; 1(1):e00045–15. https://doi.org/10.1128/mSphere.00045-15 PMID: 27239562

61. Dubois T, Tremblay YDN, Hamiot A, Martin-Verstraete I, Deschamps J, Monot M, et al. A microbiota-generated bile salt induces biofilm formation in Clostridium difficile. NPJ Biofilms Microbiomes. 2019; 5 (1):14. https://doi.org/10.1038/s41522-019-0087-4 PMID: 31098293

62. Oberkampf M, Hamiot A, Altamirano-Silva P, Bellés-Sancho P, Tremblay YDN, DiBenedetto N, et al. c-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by Clostridioides difficile. Sci Signal. 2022 Sep 6; 15(750):eabn8171. https://doi.org/10.1126/scisignal.abn8171 PMID: 36067333

63. Cremers CM, Knoefler D, Vitvitsky V, Banerjee R, Jakob U. Bile salts act as effective protein-unfolding agents and instigators of disulfide stress in vivo. Proc Natl Acad Sci U S A. 2014 Apr 22; 111(16): E1610–9. https://doi.org/10.1073/pnas.1401941111 PMID: 24706920

64. Kosower NS, Kosower EM. [11] Diamide: An oxidant probe for thiols. In: Methods in Enzymology [Internet]. Elsevier; 1995 [cited 2022 Aug 1]. p. 123–33. Available from: https://linkinghub.elsevier.com/retrieve/pii/0076687995511164

65. Andreesen JR. Glycine reductase mechanism. Curr Opin Chem Biol. 2004 Oct; 8(5):454–61.

66. Lawley TD, Croucher NJ, Yu L, Clare S, Sebaihia M, Goulding D, et al. Proteomic and Genomic Characterization of Highly Infectious *Clostridium difficile* 630 Spores. J Bacteriol. 2009 Sep; 191(17):5377–86.

67. Pereira FC, Saujet L, Tomé AR, Serrano M, Monot M, Couture-Tosi E, et al. The Spore Differentiation Pathway in the Enteric Pathogen Clostridium difficile. PLoS Genet. 2013 Oct 3; 9(10):e1003782. https://doi.org/10.1371/journal.pgen.1003782 PMID: 24098139

68. Saujet L, Pereira FC, Henriques AO, Martin-Verstraete I. The regulatory network controlling spore formation in *Clostridium difficile*. FEMS Microbiol Lett. 2014 Sep; 358(1):1–10.

69. Barbut F. How to eradicate Clostridium difficile from the environment. J Hosp Infect. 2015 Apr 1; 89 (4):287–95. https://doi.org/10.1016/j.jhin.2014.12.007 PMID: 25638358

70. Marteyn B, Scorza FB, Sansonetti PJ, Tang C. Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract. Cell Microbiol. 2011; 13(2):171–6. https://doi.org/10.1111/j.1462-5822.2010.01549.x PMID: 21166974

71. Fimlaid KA, Bond JP, Schutz KC, Putnam EE, Leung JM, Lawley TD, et al. Global Analysis of the Sporulation Pathway of Clostridium difficile. PLoS Genet. 2013 Aug 8; 9(8):e1003660.

72. Garcia-Garcia T, Douché T, Gianetto QG, Poncet S, El Omrani N, Smits WK, et al. In-depth characterization of the Clostridioides difficile phosphoproteome to identify Ser/Thr kinase substrates. Mol Cell Proteomics. 2022 Oct; 10(428). https://doi.org/10.1016/j.mcpro.2022.100428 PMID: 36252736

73. McBride S. Glycine fermentation by C. difficile promotes virulence, spore formation, and is induced by host cathelicidin.

74. Andreesen JR. Glycine metabolism in anaerobes. Antonie Van Leeuwenhoek. 1994; 66(1–3):223–37. https://doi.org/10.1007/BF00871641 PMID: 7747933
75. Leslie JL, Junior ML, Vendrov KC, Standke AK, Barron MR, O'Brien TJ, et al. Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant. mBio. 2021 Mar 30; 12 (2):e00522-21. https://doi.org/10.1128/mBio.00522-21 PMID: 33785619

76. Baker LMS, Raudonikiene A, Hoffman PS, Poole LB. Essential Thioredoxin-Dependent Peroxiredoxin System from Helicobacter pylori: Genetic and Kinetic Characterization. J Bacteriol. 2001 Mar; 183 (6):1961-73. https://doi.org/10.1128/JB.183.6.1961-1973.2001 PMID: 11222594

77. Loi VV, Rossius M, Antelmann H. Redox regulation by reversible protein S-thiolation in bacteria. Front Microbiol [Internet]. 2015 Mar 16 [cited 2021 Dec 8];6. Available from: http://journal.frontiersin.org/Article/10.3389/fmicb.2015.00187/abstract. https://doi.org/10.3389/fmicb.2015.00187 PMID: 25852656

78. Reeves SA, Parsonage D, Nelson KJ, Poole LB. Kinetic and Thermodynamic Features Reveal That *Escherichia coli* BCP Is an Unusually Versatile Peroxiredoxin. Biochemistry. 2011 Oct 18; 50 (41):8970-81.

79. Baker LMS, Poole LB. Catalytic Mechanism of Thiol Peroxidase from Escherichia coli: sulfenic acid formation and overoxidation of essential Cys61*. J Biol Chem. 2003 Mar 14; 278(11):9203-11.

80. Alamuri P, Maier RJ. Methionine sulfoxide reductase in Helicobacter pylori: Interaction with methionine-rich proteins and stress-induced expression. J Bacteriol. 2006; 188(16):5839-50. https://doi.org/10.1128/JB.00430-06 PMID: 16885452

81. Hong HA, Ferreira WT, Hosseini S, Anwar S, Hitri K, Wilkinson AJ, et al. The Spore Coat Protein CotE Facilitates Host Colonization by Clostridium difficile. J Infect Dis. 2017 Dec 1; 216(11):1452-9. https://doi.org/10.1093/infdis/jix488 PMID: 28968845

82. Torrents E. Ribonucleotide reductases: essential enzymes for bacterial life. Front Cell Infect Microbiol. 2014 Apr 28; 4:52. https://doi.org/10.3389/fcimb.2014.00052 PMID: 24809024

83. Mishra S, Imlay JA. An anaerobic bacterium, Bacteroides thetaiotaomicron, uses a consortium of enzymes to scavenge hydrogen peroxide. Mol Microbiol. 2013 Dec; 90(6): https://doi.org/10.1111/mmi.12438 PMID: 24164536

84. Mallén-Ponce MJ, Huertas MJ, Florencio FJ. Exploring the Diversity of the Thioredoxin Systems in Cyanobacteria. Antioxidants. 2022 Mar 28; 11(4):654. https://doi.org/10.3390/antiox11040654 PMID: 35453339

85. Latifi A, Ruiz M, Zhang CC. Oxidative stress in cyanobacteria. FEMS Microbiol Rev. 2009 Mar 1; 33 (2):258-78. https://doi.org/10.1111/j.1574-6976.2008.00134.x PMID: 18834454

86. Herrero A, Stavans J, Flores E. The multicellular nature of filamentous heterocyst-forming cyanobacteria. FEMS Microbiol Rev. 2016 Nov 1; 40(6):831-54. https://doi.org/10.1093/femsre/fuw029 PMID: 28204529

87. Kumar K, Mella-Herrera RA, Golden JW. Cyanobacterial Heterocysts. Cold Spring Harb Perspect Biol. 2010 Apr; 2(4):a000315. https://doi.org/10.1101/cshperspect.a000315 PMID: 20452939

88. Nikkanen L, Toivola J, Diaz MG, Rintamäki E. Chloroplast thioredoxin systems: prospects for improving photosynthesis. Philos Trans R Soc B Biol Sci. 2017 Sep 26; 372(1730):20160474. https://doi.org/10.1098/rstb.2016.0474 PMID: 28808108

89. Miranda-Vizuete A, Damdimopoulos AE, Spyrou G. The Mitochondrial Thioredoxin System. Antioxid Redox Signal. 2000 Dec; 2(4):801-10. https://doi.org/10.1089/ars.2000.2.4-801 PMID: 11213484

90. Wilson KH, Kennedy MJ, Fekety FR. Use of sodium taurocholate to enhance spore recovery on a medium selective for Clostridium difficile. J Clin Microbiol. 1982 Mar; 15(3):443-6. https://doi.org/10.1128/jcm.15.3.443-446.1982 PMID: 7076817

91. Heap JT, Pennington OJ, Cartman ST, Carter GP, Minton NP. The ClosTron: a universal gene knock-out system for the genus Clostridium. J Microbiol Methods. 2007 Sep; 70(3):452-64. https://doi.org/10.1016/j.mimet.2007.05.021 PMID: 17658189

92. Peltier J, Hamiot A, Garneau JR, Boudry P, Maikova A, Hajnsdorf E, et al. Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile. Commun Biol. 2020 Nov 27; 3:718. https://doi.org/10.1038/s42003-020-01448-5 PMID: 33247281

93. Saujet L, Monot M, Dupuy B, Soutourina O, Martin-Verstraete I. The Key Sigma Factor of Transition Phase, Sigh, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile. J Bacteriol. 2011 Jul; 193(13):3186-96.

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75. Leslie JL, Junior ML, Vendrov KC, Standke AK, Barron MR, O'Brien TJ, et al. Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant. mBio. 2021 Mar 30; 12 (2):e00522-21. https://doi.org/10.1128/mBio.00522-21 PMID: 33785619

76. Baker LMS, Raudonikiene A, Hoffman PS, Poole LB. Essential Thioredoxin-Dependent Peroxiredoxin System from Helicobacter pylori: Genetic and Kinetic Characterization. J Bacteriol. 2001 Mar; 183 (6):1961-73. https://doi.org/10.1128/JB.183.6.1961-1973.2001 PMID: 11222594

77. Loi VV, Rossius M, Antelmann H. Redox regulation by reversible protein S-thiolation in bacteria. Front Microbiol [Internet]. 2015 Mar 16 [cited 2021 Dec 8];6. Available from: http://journal.frontiersin.org/Article/10.3389/fmicb.2015.00187/abstract. https://doi.org/10.3389/fmicb.2015.00187 PMID: 25852656

78. Reeves SA, Parsonage D, Nelson KJ, Poole LB. Kinetic and Thermodynamic Features Reveal That *Escherichia coli* BCP Is an Unusually Versatile Peroxiredoxin. Biochemistry. 2011 Oct 18; 50 (41):8970-81.

79. Baker LMS, Poole LB. Catalytic Mechanism of Thiol Peroxidase from Escherichia coli: sulfenic acid formation and overoxidation of essential Cys61*. J Biol Chem. 2003 Mar 14; 278(11):9203-11.

80. Alamuri P, Maier RJ. Methionine sulfoxide reductase in Helicobacter pylori: Interaction with methionine-rich proteins and stress-induced expression. J Bacteriol. 2006; 188(16):5839-50. https://doi.org/10.1128/JB.00430-06 PMID: 16885452

81. Hong HA, Ferreira WT, Hosseini S, Anwar S, Hitri K, Wilkinson AJ, et al. The Spore Coat Protein CotE Facilitates Host Colonization by Clostridium difficile. J Infect Dis. 2017 Dec 1; 216(11):1452-9. https://doi.org/10.1093/infdis/jix488 PMID: 28968845

82. Torrents E. Ribonucleotide reductases: essential enzymes for bacterial life. Front Cell Infect Microbiol. 2014 Apr 28; 4:52. https://doi.org/10.3389/fcimb.2014.00052 PMID: 24809024

83. Mishra S, Imlay JA. An anaerobic bacterium, Bacteroides thetaiotaomicron, uses a consortium of enzymes to scavenge hydrogen peroxide. Mol Microbiol. 2013 Dec; 90(6): https://doi.org/10.1111/mmi.12438 PMID: 24164536

84. Mallén-Ponce MJ, Huertas MJ, Florencio FJ. Exploring the Diversity of the Thioredoxin Systems in Cyanobacteria. Antioxidants. 2022 Mar 28; 11(4):654. https://doi.org/10.3390/antiox11040654 PMID: 35453339

85. Latifi A, Ruiz M, Zhang CC. Oxidative stress in cyanobacteria. FEMS Microbiol Rev. 2009 Mar 1; 33 (2):258-78. https://doi.org/10.1111/j.1574-6976.2008.00134.x PMID: 18834454

86. Herrero A, Stavans J, Flores E. The multicellular nature of filamentous heterocyst-forming cyanobacteria. FEMS Microbiol Rev. 2016 Nov 1; 40(6):831-54. https://doi.org/10.1093/femsre/fuw029 PMID: 28204529

87. Kumar K, Mella-Herrera RA, Golden JW. Cyanobacterial Heterocysts. Cold Spring Harb Perspect Biol. 2010 Apr; 2(4):a000315. https://doi.org/10.1101/cshperspect.a000315 PMID: 20452939

88. Nikkanen L, Toivola J, Diaz MG, Rintamäki E. Chloroplast thioredoxin systems: prospects for improving photosynthesis. Philos Trans R Soc B Biol Sci. 2017 Sep 26; 372(1730):20160474. https://doi.org/10.1098/rstb.2016.0474 PMID: 28808108

89. Miranda-Vizuete A, Damdimopoulos AE, Spyrou G. The Mitochondrial Thioredoxin System. Antioxid Redox Signal. 2000 Dec; 2(4):801-10. https://doi.org/10.1089/ars.2000.2.4-801 PMID: 11213484

90. Wilson KH, Kennedy MJ, Fekety FR. Use of sodium taurocholate to enhance spore recovery on a medium selective for Clostridium difficile. J Clin Microbiol. 1982 Mar; 15(3):443-6. https://doi.org/10.1128/jcm.15.3.443-446.1982 PMID: 7076817

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97. Mooyottu S, Flock G, Venkitanarayanan K. Carvacrol reduces Clostridium difficile sporulation and spore outgrowth in vitro. J Med Microbiol. 2017; 66(8):1229-34. https://doi.org/10.1099/jmm.0.000515 PMID: 28786786

98. Malyshev D, Jones IA, McKracken M, Öberg R, Harper GM, Joshi LT, et al. Hypervirulent R20291 Clostridioides difficile spores show disinfection resilience to sodium hypochlorite despite structural changes. BMC Microbiol. 2023 Mar 6; 23(1):59. https://doi.org/10.1186/s12866-023-02787-z PMID: 36879193

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102. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8; 11:119. https://doi.org/10.1186/1471-2105-11-119 PMID: 20211023

103. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020 May 1; 37(5):1530-4. https://doi.org/10.1093/molbev/msaa015 PMID: 32011700

104. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017 Jun; 14(6):587-9. https://doi.org/10.1038/nmeth.4285 PMID: 28481363

105. Chernomor O, von Haeseler A, Minh BQ. Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst Biol. 2016 Nov; 65(6):997-1008. https://doi.org/10.1093/sysbio/syw037 PMID: 27121966

106. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol. 2018 Feb 1; 35(2):518-22. https://doi.org/10.1093/molbev/msx281 PMID: 29077904

107. Lemoine F, Gascuel O. Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows. NAR Genomics Bioinforma. 2021 Sep;3(3):Iqab075.

108. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11; 7:539.

109. Gouy M, Guindon S, Gascuel O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010 Feb; 27(2):221-4. https://doi.org/10.1093/molbev/msp259 PMID: 19854763

110. Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol. 2016 Jun; 33(6):1635-8. https://doi.org/10.1093/molbev/msw046 PMID: 26921390

111. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 2012 Dec 1; 61(6):1061-7. https://doi.org/10.1093/sysbio/sys062 PMID: 22780991

112. Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol. 2013 Apr 1; 30(4):772-80. https://doi.org/10.1093/molbev/mst010 PMID: 23329690

113. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009 May 1; 25(9):1189-91. https://doi.org/10.1093/bioinformatics/btp033 PMID: 19151095

114. Valette O, Tran TTT, Cavazza C, Caudeville E, Brasseur G, Dolla A, et al. Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris. Front Microbiol. 2017 Sep 29; 8:1855. https://doi.org/10.3389/fmicb.2017.01855 PMID: 29033913
96. Dembek M, Stabler RA, Witney AA, Wren BW, Fairweather NF. Transcriptional Analysis of Temporal Gene Expression in Germinating Clostridium difficile 630 Endospores. PLoS ONE. 2013 May 15; 8(5): e64011. https://doi.org/10.1371/journal.pone.0064011 PMID: 23691138

97. Mooyottu S, Flock G, Venkitanarayanan K. Carvacrol reduces Clostridium difficile sporulation and spore outgrowth in vitro. J Med Microbiol. 2017; 66(8):1229-34. https://doi.org/10.1099/jmm.0.000515 PMID: 28786786

98. Malyshev D, Jones IA, McKracken M, Öberg R, Harper GM, Joshi LT, et al. Hypervirulent R20291 Clostridioides difficile spores show disinfection resilience to sodium hypochlorite despite structural changes. BMC Microbiol. 2023 Mar 6; 23(1):59. https://doi.org/10.1186/s12866-023-02787-z PMID: 36879193

99. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009 Jun 1; 25 (11):1422-3. https://doi.org/10.1093/bioinformatics/btp163 PMID: 19304878

100. Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2016 Jan 4; 44(D1):D67-72.

101. Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. NAR Genomics Bioinforma. 2021 Mar; 3(1):Iqaa106. https://doi.org/10.1093/nargab/lqaa106 PMID: 33575648

102. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8; 11:119. https://doi.org/10.1186/1471-2105-11-119 PMID: 20211023

103. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020 May 1; 37(5):1530-4. https://doi.org/10.1093/molbev/msaa015 PMID: 32011700

104. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017 Jun; 14(6):587-9. https://doi.org/10.1038/nmeth.4285 PMID: 28481363

105. Chernomor O, von Haeseler A, Minh BQ. Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst Biol. 2016 Nov; 65(6):997-1008. https://doi.org/10.1093/sysbio/syw037 PMID: 27121966

106. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol. 2018 Feb 1; 35(2):518-22. https://doi.org/10.1093/molbev/msx281 PMID: 29077904

107. Lemoine F, Gascuel O. Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows. NAR Genomics Bioinforma. 2021 Sep;3(3):Iqab075.

108. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11; 7:539.

109. Gouy M, Guindon S, Gascuel O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2010 Feb; 27(2):221-4. https://doi.org/10.1093/molbev/msp259 PMID: 19854763

110. Huerta-Cepas J, Serra F, Bork P. ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. Mol Biol Evol. 2016 Jun; 33(6):1635-8. https://doi.org/10.1093/molbev/msw046 PMID: 26921390

111. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol. 2012 Dec 1; 61(6):1061-7. https://doi.org/10.1093/sysbio/sys062 PMID: 22780991

112. Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol. 2013 Apr 1; 30(4):772-80. https://doi.org/10.1093/molbev/mst010 PMID: 23329690

113. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009 May 1; 25(9):1189-91. https://doi.org/10.1093/bioinformatics/btp033 PMID: 19151095

114. Valette O, Tran TTT, Cavazza C, Caudeville E, Brasseur G, Dolla A, et al. Biochemical Function, Molecular Structure and Evolution of an Atypical Thioredoxin Reductase from Desulfovibrio vulgaris. Front Microbiol. 2017 Sep 29; 8:1855. https://doi.org/10.3389/fmicb.2017.01855 PMID: 29033913