Safe Haskell | None |
---|---|

Language | Haskell98 |

- gsc :: Dendrogram a -> Dendrogram (a, Distance)

# Documentation

gsc :: Dendrogram a -> Dendrogram (a, Distance) Source

*O(n^2)* Calculates the Gerstein/Sonnhammer/Chothia
weights for all elements of a dendrogram. Weights are
annotated to the leafs of the dendrogram while distances in
branches are kept unchanged.

Distances `d`

in branches should be non-increasing and between
`0`

(in the leafs) and `1`

. The final weights are normalized
to average to `1`

(i.e. sum to the number of sequences, the
same they would sum if all weights were `1`

).

For example, suppose we have

dendro = Branch 0.8 (Branch 0.5 (Branch 0.2 (Leaf`A`

) (Leaf`B`

)) (Leaf`C`

)) (Leaf`D`

)

This is the same as GSC paper's example, however they used
similarities while we are using distances (i.e. applying
`(1-)`

to the distances would give exactly their example).
Then `gsc dendro`

is

gsc dendro == Branch 0.8 (Branch 0.5 (Branch 0.2 (Leaf (`A`

,0.7608695652173914)) (Leaf (`B`

,0.7608695652173914))) (Leaf (`C`

,1.0869565217391306))) (Leaf (`D`

,1.3913043478260871))

which is exactly what they calculated.