For each transcript, we have generated a file
$(gene_name).$(transcript_id).sitewise which gives results relating to
each site of each transcript, from the SLR and BEB analyses.  The file
has one line for each codon of the transcript alignment, containing the
following entries:

align_site  plot_site  human_site  Pvalue_+seln_BEB  omega_BEB  omega_SLR  Pvalue_uncorr_+seln_SLR  Pvalue_+seln_SLR  Pvalue_uncorr_nonneut_SLR  Pvalue_nonneut_SLR

It will help to read the introductory stuff at the start of the
explain.summary file before you read on here.  That said:

align_site
  Codon site in the transcript multiple alignment.

plot_site
  Nucleotide site in the multi-transcript plots
  $(gene_name).$(gene_id).$(METHOD).pdf

human_site
  Nucleotide site in the Encode human sequence.

Pvalue_+seln_BEB
  BEB p-value for test of whether the codon is evolving under positive
  selection (omega>1).

omega_BEB
  BEB value of omega for the site

omega_SLR
  SLR value of omega for the site

Pvalue_uncorr_+seln_SLR
  Uncorrected p-value under SLR for test of whether codon is evolving
  under positive selection (does not allow for multiple testing, i.e. of
  all sites in the transcript)

Pvalue_+seln_SLR
  Corrected p-value under SLR for test of whether codon is evolving
  under positive selection (makes allowance for multiple testing,
  i.e. of all sites in the transcript)

Pvalue_uncorr_nonneut_SLR
  Uncorrected p-value under SLR for test of whether codon is evolving
  non-neutrally (omega!=1) (does not allow for multiple testing, i.e. of
  all sites in the transcript)

Pvalue_nonneut_SLR
  Ccorrected p-value under SLR for test of whether codon is evolving
  non-neutrally (omega!=1) (makes allowance for multiple testing,
  i.e. of all sites in the transcript)