Likelihood ratio tests for positive selection on specific sites by PAML and HyPhy.

#seq, number of nucleotide sequence entries used in the multi-alignments. Length, nucleotide sequence length in alignment. PSS, positive-selected site, predicted by FEL with cutoff of PP>0.90 or BEB posterior probability (in M8 by PAML) of P>0.90. p1 is proportion of sites in the class with ω>1 and ω1 is the estimate of ω for that class. Numbers in parentheses are codon positions in the alignment. Df, degree of freedom in the LRT. Only significant P values in the LRT are presented in bold.*, positive selected sites predicted by different methods are overlapping.

#seq：多序列比对中使用的核苷酸序列条目数。Length：比对中的核苷酸序列长度。PSS：正选择位点（positive-selected site），指通过FEL以PP>0.90为阈值预测得到，或是通过PAML的M8模型中BEB后验概率P>0.90计算得到的位点。p1为ω>1的位点类别所占比例，ω1为该类别ω值的估计值。括号内的数字为比对序列中的密码子位置。Df：似然比检验（likelihood ratio test, LRT）的自由度。仅将似然比检验中具有统计学显著性的P值以粗体标注。*：不同方法预测得到的正选择位点存在重叠。