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Table 1 Conditions used in simulations for 24 models of the GTR family.

From: Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets

Simulation Parameter set Tree height Ntaxa Nchar Simulation software No.
I A 0.7 30 1000 Seq-Gen I-1
  A 0.5 30 1000 Seq-Gen I-2
  A 0.3 30 1000 Seq-Gen I-3
  A 0.1 30 1000 Seq-Gen I-4
  B 0.7 30 1000 Seq-Gen I-5
  B 0.5 30 1000 Seq-Gen I-6
  B 0.3 30 1000 Seq-Gen I-7
  B 0.1 30 1000 Seq-Gen I-8
II A 0.5 22 1000 Seq-Gen II-1
  A 0.5 50 1000 Seq-Gen II-2
III A 0.5 22 1000 Mesquite III-1
IV A Nonclock 22 1000 Seq-Gen IV-1
V A 0.5 30 300 Seq-Gen V-1
  A 0.5 30 2000 Sen-Gen V-2
  1. One hundred replicates were performed for each set of conditions. The models consisted of JC (0) [61], K80 (1) [62], SYM (5) [63], F81 (3) [64], HKY (4) [65, 66], GTR (8) [67], JC + I (1), K80 + I (2), SYM + I (6), F81 + I (4), HKY + I (4), GTR + I (9), JC + Γ (1), K80 + Γ (2), SYM + Γ (6), F81 + Γ (4), HKY + Γ (4), GTR + Γ (9), JC + I + Γ (2), K80 + I + Γ (3), SYM + I + Γ (7), F81 + I + Γ (5), HKY + I + Γ (5) and GTR + I + Γ (10), where 'I' represents the proportion of invariable sites, 'Γ' represents the discrete gamma distribution with four rate categories, and number in parentheses is the number of free parameters of each model. One classification of the 24 models was to put them into four categories: base (JC, K80, etc.), base + I (JC + I, K80 + I, etc.), base + Γ (JC + Γ, K80 + Γ, etc.) and base + I + Γ (JC + I + Γ, K80 + I + Γ, etc.). The other was that models with the same number of free parameters were grouped together, resulting in a total of 11 categories. In addition, we called every four models having the same parameters in the substitution-rate matrix as base-like models (e.g., the four models of SYM, SYM + I, SYM + Γ, SYM + I + Γ were called as SYM-like models).