Description of statistics on Monte Carlo results page:

1. non-reference name: Non-reference sequence name. Each table row lists statistics for a reference sequence versus non-reference sequence pairwise sequence comparison.
   
   
2. # nt used: Number of nucleotides used to calculate the log likelihood scores. This will depend on the nucleotide range selected on the initial MLOGD server page, and will be reduced if any nucleotide positions are omitted due to gaps or ambiguous nt codes (in either sequence), or stop to non-stop transitions (in either the null or alternate models).
   
   
3. divergence (mean muts per nt): Pairwise sequence divergence (mean number of point differences per nucleotide). (I.e. all nucleotide positions mutation fraction.)
   
   
4. MLOGD ln(LR) per nt: The sum of the null versus alternate model log likelihood ratios over the whole pairwise sequence comparison, divided by the number of nucleotides used.
   
   
5. frac syn muts: Fraction of the aligned codons, within the null model CDSs, that are different between the two sequences but code for identical amino acids. (I.e. synonymous codon mutation fraction.)
   
   
6. frac nonsyn muts: Fraction of the aligned codons, within the null model CDSs, that are different between the two sequences and code for different amino acids. (I.e. nonsynonymous codon mutation fraction.)
   
   
7. frac N1 muts: Fraction of the 1st codon position nucleotides (e.g. the C in CAG gln), within the null model CDSs, that are different between the two sequences. (I.e. 1st codon position mutation fraction.)
   
   
8. frac N2 muts: Fraction of the 2nd codon position nucleotides (e.g. the A in CAG gln), within the null model CDSs, that are different between the two sequences. (I.e. 2nd codon position mutation fraction.)
   
   
9. frac N3 muts: Fraction of the 3rd codon position nucleotides (e.g. the G in CAG gln), within the null model CDSs, that are different between the two sequences. (I.e. 3rd codon position mutation fraction.)
   
   
10. MLOGD ln(LR): Null versus alternate model log likelihood ratio for the MLOGD statistic, estimated by comparing the observed value with simulated distributions.
    
    
11. syn ln(LR): Null versus alternate model log likelihood ratio for the 'frac syn muts' statistic, estimated by comparing the observed value with simulated distributions.
    
    
12. nonsyn ln(LR): Null versus alternate model log likelihood ratio for the 'frac nonsyn muts' statistic, estimated by comparing the observed value with simulated distributions.
    
    
13. N1 ln(LR): Null versus alternate model log likelihood ratio for the 'frac N1 muts' statistic, estimated by comparing the observed value with simulated distributions.
    
    
14. N2 ln(LR): Null versus alternate model log likelihood ratio for the 'frac N2 muts' statistic, estimated by comparing the observed value with simulated distributions.
    
    
15. N3 ln(LR): Null versus alternate model log likelihood ratio for the 'frac N3 muts' statistic, estimated by comparing the observed value with simulated distributions.
    
    

Notes:

• If the null model is non-coding (no 'Known CDSs' entered) then columns 5-9 will all be 0.00 and columns 11-15 will all be 99999.0.
• For columns 10-15, see Firth A. E., Brown C. M., 2005, Bioinformatics, 21, 282-92 and Section 2.5 of the Supplementary Material pdf file (1.0MB), ps file (0.9MB) for details of this calculation.
• If the entire nucleotide range selected on the initial MLOGD server page is coding in the null model, then the average of columns 7, 8 and 9 should equal column 2, while the average of columns 5 and 6 would generally be larger since these statistics count mutated codons rather than single nucleotides.
• Multiplying columns 2 and 4 gives the null versus alternate model log likelihood ratio summed over the whole pairwise sequence comparison. In principal this is the same statistic as in column 10. However, there will generally be significant disagreement due to the approximations made in the calculation of the column 10 statistic (details).