CaiResult.php
Immutable value object holding the outcome of a Codon Adaptation Index calculation Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 2 October 2026
Table of Contents
Classes
- CaiResult
- The score is the geometric mean of relative synonymous codon usage across every SCORED codon of the coding sequence, ranging from just above 0 (uses almost nothing but rare codons) to 1 (uses the most frequent codon for every amino acid). codonsScored is how many codons that geometric mean was actually taken over, after excluding stop codons and every amino acid with no synonym (Met, Trp under the standard genetic code) - useful to judge how statistically meaningful the score is for a short coding sequence.