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Table 1 dS/dN calculations for phenylalanine ammonia-lyase (PAL) contigs

From: Validation of an NSP-based (negative selection pattern) gene family identification strategy

Comparison Sda Sn S N ps pn ds dn ds/dn ps/pn
Contig1 Contig4 38.50 18.50 62.83 219.17 0.61 0.08 1.27 0.09 14.22 7.26
Contig1 Contig3 42.17 39.83 65.17 216.83 0.65 0.18 1.49 0.21 7.07 3.52
Contig1 Contig9 42.33 36.67 65.50 216.50 0.65 0.17 1.48 0.19 7.73 3.82
Contig1 Contig6 52.50 138.50 63.33 197.67 0.83 0.70 NA 0.00 NA 1.18
Contig1 Contig8 53.50 138.50 63.33 197.67 0.84 0.70 NA 0.00 NA 1.21
Contig1 Contig7 45.17 153.83 62.83 210.17 0.72 0.73 2.39 2.80 0.85 0.98
Contig4 Contig3 211.83 133.17 286.33 985.67 0.74 0.14 3.22 0.15 21.64 5.48
Contig4 Contig9 143.00 105.00 191.67 639.33 0.75 0.16 3.94 0.19 21.27 4.54
Contig4 Contig6 152.50 490.50 201.50 665.50 0.76 0.74 NA 0.00 NA 1.03
Contig4 Contig8 80.33 225.67 99.83 314.17 0.80 0.72 NA 0.00 NA 1.12
Contig4 Contig7 65.00 233.00 93.17 326.83 0.70 0.71 2.00 2.25 0.89 0.98
Contig3 Contig9 1.50 14.50 197.17 633.83 0.01 0.02 0.01 0.02 0.33 0.33
Contig3 Contig6 160.50 486.50 206.83 660.17 0.78 0.74 NA 0.00 NA 1.05
Contig3 Contig8 81.83 222.17 102.83 311.17 0.80 0.71 NA 0.00 NA 1.11
Contig3 Contig7 70.50 228.50 96.00 324.00 0.73 0.71 2.90 2.11 1.37 1.04
Contig9 Contig6 150.00 454.00 196.17 613.83 0.76 0.74 NA 0.00 NA 1.03
Contig9 Contig8 81.33 220.67 103.17 310.83 0.79 0.71 NA 0.00 NA 1.11
Contig9 Contig7 71.67 229.33 96.33 323.67 0.74 0.71 3.61 2.17 1.66 1.05
Contig6 Contig8 2.00 4.00 108.33 305.67 0.02 0.01 0.02 0.01 1.42 1.41
Contig6 Contig7 68.33 200.67 97.50 301.50 0.70 0.67 2.04 1.64 1.25 1.05
Contig8 Contig7 68.33 199.67 97.50 301.50 0.70 0.66 2.04 1.61 1.27 1.06
  1. SNAP output results for all 21 pairwise comparisons of 7 contigs in which an ORF was identified. A ds/dn value greater than 2.00 was chosen as threshold to indicate contigs that potentially represent distinct gene family members.
  2. a – See http://www.hiv.lanl.gov for explanation of abbreviations and calculations.