... ... @@ -48,7 +48,7 @@ Sequences $S'$ and $T'$ are then subjected to a second procedure that finds s_\text{\tiny DCJ}(S'', T'') = \sum_{C \in \mathcal{C}}{f(|C|)} + \frac{1}{2} \left (\sum_{O \in \mathcal{O}}{f(|O|+1)} + \sum_{E \in \mathcal{E}}{f(|E|+2)}\right) - d \cdot p\:,  where $\mathcal{C}$, $\mathcal{O}$ and $\mathcal{E}$ are the sets of cycles, odd paths, and even paths in the constructed adjacency graph of $S''$ and $T''$, and $d := |S|+|T|-(|S''|+|T''|)$ is the number of deleted markers. Function $f : 2\mathbb{N} \rightarrow \mathbb{R}$ scores each cycle and path proportional to its length. Because short cycles and paths are indicators of similarity, whereas long cycles and paths suggest the opposite, Gecko3-DCJ uses a simple realization of $f$ that works well in general: where $\mathcal{C}$, $\mathcal{O}$ and $\mathcal{E}$ are the sets of cycles, odd paths, and even paths in the constructed adjacency graph of $S''$ and $T''$, $d := |S|+|T|-(|S''|+|T''|)$ is the number of deleted markers and $p$ is the deletion penalty. Function $f : 2\mathbb{N} \rightarrow \mathbb{R}$ scores each cycle and path proportional to its length. Because short cycles and paths are indicators of similarity, whereas long cycles and paths suggest the opposite, Gecko3-DCJ uses a simple realization of $f$ that works well in general: math f(l) = \frac{2 - l}{b - 2} + 1\:. ... ...