Jukes-Cantor (JC69) Substitution Model
This release introduces the first substitution model to the project with support for the Jukes–Cantor (JC69) evolutionary distance calculation.
Until now the Distance Matrix Calculator supported Hamming distance and proportional distance (p-distance), both of which measure observed sequence differences. This release extends the calculator to estimate evolutionary distance by correcting for multiple substitutions that may have occurred at the same nucleotide position over time.
Highlights
Jukes–Cantor (JC69) Distance
The Distance Matrix Calculator now supports the Jukes–Cantor substitution model.
This model estimates the expected number of substitutions per site, providing a corrected evolutionary distance that accounts for hidden mutation events not directly observable from aligned sequences.
The calculator now supports three distance calculations:
- Hamming distance
- Proportional distance (p-distance)
- Jukes–Cantor (JC69)
The desired calculation can be selected using the existing --distance-type command-line option.
Improved Documentation
The project documentation has been expanded to describe the Jukes–Cantor model, including:
- Mathematical background
- Model assumptions
- Sequence saturation
- Updated usage examples
The Wiki Home page has also been updated to reflect the expanded functionality.
Why this matters
This release represents an important milestone in the project’s evolution.
Previous releases focused on simulating sequence evolution and measuring observed genetic differences. This release introduces the first model-based estimate of evolutionary distance, providing a more realistic representation of sequence divergence over time.
This lays the groundwork for the next stage of the project: reconstructing phylogenetic trees from corrected evolutionary distance matrices using algorithms such as UPGMA.