The intron type was defined as follows: type 0, lies between two codons; type I, lies after the first base in the codon; type II, lies after the second base in the codon.
The pathway between two codons was calculated as the average number of silent and replacement changes from all possible paths between the pair.
Of the 74 intron positions, 25 are in phase zero (between two codons), 27 are in phase one (between the first et second base of a codon) and 22 are in phase two (between the second and third base of a codon).
Extending the distance between two codons (1 3, 1 4, 1 10) decreased the RDCU correlation.
In addition, nucleotide transitions between two codons are more likely to be synonymous especially at the third codon positions, underestimation of κ leads to underestimation of S.
Insertions and deletions can occur between two codons (in phase 0), or after the first or second nucleotide of a codon (in phase 1 and 2, respectively).
Since κ decrease is related to the reduction of substitution rate between two codons, underestimation of κ leads to underestimation of Sd.
We also classified the splice sites into three phases according to their positions in the codons: phase 0 for a splice site lying between two codons, phase 1 for a splice site lying one base inside a codon in the 3' direction, and phase 2 for a splice site lying two bases inside the codon in the 3' direction.
On the other hand, avoidance of the UA dinucleotide between two codons also has a role here, because out-frame UGA stop-codons were not observed in any of the conserved biased dicodon pairs.
The intron phase distribution in the catalytic domain of nematode GHF5 cellulases was biased towards phase 0; 16 out of the 24 introns (66%) were inserted in between two codons.
