Commit c633b0b7 authored by Diego Rubert's avatar Diego Rubert

Update README.md

parent b61c9827
......@@ -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\:.
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment