PRANK can align sequences using a “structure model” that describes multiple evolutionary processes and infer regions evolving under each process along with the alignment. PRANK imports these alignment ...

Additionally, our model helps account for length, position, and abundance biases when calculating outliers in a particular message in two ways: First, we include message‐specific codon dwell times, ...

It is pertinent to note that there is only one diagram, a phylogeny, that appears in Darwin’s seminal work, “The Origin of Species.” This, ... Thus, codon model usage may serve as an important asset ...

Motivation: Codon optimization of Open Reading Frame (ORF) sequences is essential for enhancing mRNA stability and expression in applications like mRNA vaccines, where codon choice can significantly ...

The core of HELM lies in its hierarchical encoding approach, which integrates the codon structure directly into the language model’s training. This involves using a Hierarchical Cross-Entropy (HXE) ...