Parameter identification	Salt type and concentration	Base pairs handled by this set	Parameter set description	Recommendations for this set
1	DNA AOP-CMB	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	optimized parameters AOP-CMB from Weber 2015 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Recommended set for DNA. Note that parameters for mismatches and inosine are not yet optimized.
2	DNA AOP-MM-60	[Na+] 60 mM	all	optimized parameters AOP-MM-60 from Martins 2023 (unpublished), includes AOP-OW04-69 for canonical base-pairs.	Low salt concentration, this is the only parameter set that covers all types of mismatches up to trimers.
3	DNA AOP-OW04-69	[Na+] 69 mM	AT, CG	optimized parameters AOP-OW04-69 from Weber 2015 based on data by Owczarzy 2004
4	DNA AOP-OW04-119	[Na+] 119 mM	AT, CG	optimized parameters AOP-OW04-119 from Weber 2015 based on data by Owczarzy 2004
5	DNA AOP-OW04-220	[Na+] 220 mM	AT, CG	optimized parameters AOP-OW04-220 from Weber 2015 based on data by Owczarzy 2004
6	DNA AOP-OW04-621	[Na+] 621 mM	AT, CG	optimized parameters AOP-OW04-621 from Weber 2015 based on data by Owczarzy 2004
7	DNA P-SL96	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	original parameters from SantaLucia 1996 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	This set was later replaced by the P-SL98 set. Use this if you would like to get results to check with papers which use this particular set of parameters.
8	DNA AOP-SL96	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	parameters from Weber 2015 based on data by SantaLucia 1996, and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Not recommended, prefer set AOP-CMB.
9	DNA P-SG96	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	original parameters from Sugimoto 1996 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Use this if you would like to get results to check with papers which use this particular set of parameters.
10	DNA P-SL98	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	original parameters from SantaLucia 1998 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Commonly known as the unified parameter set, or SantaLucia parameters, it is widely used in the literature and bioinformatics software. Use this if you would like to get results to check with papers or software that use this set of parameters.
11	DNA AOP-SL98	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	parameters from Weber 2015 based on data by SantaLucia 1998 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Not recommended, prefer set AOP-CMB.
12	DNA P-SL04	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	original parameters from SantaLucia and Hicks 2004 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	A more recent but less known version of the unified parameter set (P-SL98). The main difference to the P-SL98 are the initiation parameters and the parameters for AA/TT.
13	DNA P-BS86	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	original parameters from Breslauer 1986 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Only use if you need to check against articles of that period. We use initiation entropy of -17.5 instead of initiation energy 5 kcal and symmetry correction entropy of -1.4 instead of 0.4 kcal of the original paper.
14	DNA P-TN04	[Na+] 1000 mM	AT, CG, AA, CC, GG, TT, GT, AC, CT, AG, IC, IA, IT, IG, II	original parameters from Tanaka 2004 and non-optimized parameters for single mismatches: Peyret 1999 original, Allawi 1997 original, Allawi 1998 original, Allawi 1998b original, Allawi 1998c original, for deoxyinosine Watkins and SantaLucia 2005 original	Use if you need to check for results that use the parameters from Tanaka 2004
15	RNA P-XIA98	[Na+] 1000 mM	AU, CG, GU	original parameters from Xia 1998 and original parameters for GU Chen 2012	Currently the standard parameter set for RNA, includes parameters for GU mismatches from Table 3 of Chen 2012 (except GGUC/CUGG).
16	RNA P-FR86	[Na+] 1000 mM	AU, CG	original parameters from Freier 1986	Use this if you would like to get results compatible with the original papers.
17	RNA AOP-VIFRW-71	[Na+] 71 mM	AU, CG	optimized parameters Ferreira et al. 2019	Recommended for RNA at [Na+] 71 mM
18	RNA AOP-VIFRW-121	[Na+] 121 mM	AU, CG	optimized parameters Ferreira et al. 2019	Recommended for RNA at [Na+] 121 mM
19	RNA AOP-VIFRW-221	[Na+] 221 mM	AU, CG	optimized parameters Ferreira et al. 2019	Recommended for RNA at [Na+] 221 mM
20	RNA AOP-VIFRW-621	[Na+] 621 mM	AU, CG	optimized parameters Ferreira et al. 2019	Recommended for RNA at [Na+] 621 mM
21	RNA AOP-VIFRW-1021	[Na+] 1021 mM	AU, CG	optimized parameters Ferreira et al. 2019	Recommended for RNA at [Na+] 1021 mM
22	RNA AOP-FIFRW-71	[Na+] 71 mM	AU, CG	optimized parameters Ferreira et al. 2019, uses the same initiation parameters as Xia 1998
23	RNA AOP-FIFRW-121	[Na+] 121 mM	AU, CG	optimized parameters Ferreira et al. 2019, uses the same initiation parameters as Xia 1998
24	RNA AOP-FIFRW-221	[Na+] 221 mM	AU, CG	optimized parameters Ferreira et al. 2019, uses the same initiation parameters as Xia 1998
25	RNA AOP-FIFRW-621	[Na+] 621 mM	AU, CG	optimized parameters Ferreira et al. 2019, uses the same initiation parameters as Xia 1998
26	RNA AOP-FIFRW-1021	[Na+] 1021 mM	AU, CG	optimized parameters Ferreira et al. 2019, uses the same initiation parameters as Xia 1998
27	DNA-RNA AOP-DRFT	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	optimized parameters from Barbosa et al. 2019 based on curve-fit data by Sugimoto 1995, Ratmeyer 1994 and Wu 2002	optimized parameters from Barbosa et al. 2019
28	DNA-RNA AOP-DRVH	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	optimized parameters from Barbosa et al. 2019 based on Van't Hoff plot data by Sugimoto 1995, Ratmeyer 1994 and Wu 2002	optimized parameters from Barbosa et al. 2019
29	DNA-RNA AOP-DRLS	[Na+] 100 mM	dArU, dCrG, dTrA, dGrC	low salt optimized parameters from Barbosa et al. 2019 based on data by Lesnik 1995
30	DNA-RNA P-SG95	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	original parameters from Sugimoto 1995	Not recommended, prefer set AOP-DRC17.
31	DNA-RNA P-BN21	[Na+] 100 mM	dArU, dCrG, dTrA, dGrC	original parameters from Banerjee 2021	These is a correction to the parameters from Banerjee 2020.
32	DNA-RNA P-BN21-S3	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	original parameters from table S3 of Banerjee 2021	These is a correction to the parameters from Banerjee 2020.
33	RNA-DNA AOP-DRFT	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	optimized parameters from Barbosa et al. 2019 based on curve-fit data by Sugimoto 1995, Ratmeyer 1994 and Wu 2002	optimized parameters from Barbosa et al. 2019
34	RNA-DNA AOP-DRVH	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	optimized parameters from Barbosa et al. 2019 based on Van't Hoff plot data by Sugimoto 1995, Ratmeyer 1994 and Wu 2002	optimized parameters from Barbosa et al. 2019
35	RNA-DNA AOP-DRLS	[Na+] 100 mM	dArU, dCrG, dTrA, dGrC	low salt optimized parameters from Barbosa et al. 2019 based on data by Lesnik 1995
36	RNA-DNA P-SG95	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	original parameters from Sugimoto 1995	Not recommended, prefer set AOP-DRC17.
37	RNA-DNA P-BN21	[Na+] 100 mM	dArU, dCrG, dTrA, dGrC	original parameters from Banerjee 2021	These is a correction to the parameters from Banerjee 2020.
38	RNA-DNA P-BN21-S3	[Na+] 1000 mM	dArU, dCrG, dTrA, dGrC	original parameters from table S3 of Banerjee 2021	These is a correction to the parameters from Banerjee 2020.
39	LNA:DNA-DNA AOP-LNA	[Na+] 1021 mM	+AT, A+T, +CG, C+G, AT, CG	optimized parameters for single LNA modifications in DNA-DNA Ferreira 2023 (unpublished)	recommended Ferreira 2023 (unpublished).
40	LNA:DNA-DNA P-OW11-T2	[Na+] 1021 mM	+AT, A+T, +CG, C+G, AT, CG	parameters for single LNA modifications in DNA-DNA Owczarzy 2011, DNA parameters are from set AOP-SL98.	Owczarzy 2011.