@@ -4,7 +4,7 @@ Gene and regulator input files can be formatted as [simple lists](ListFile).
However, to represent subclustering in a tree structure, XML can be used.
The parent element is `ModuleNetwork`, it's children being `Module`s with an `id` attribute and an optional `name` attribute.
A module has a `GeneTree` which contains a tree structure of `Child` elements, either with `node` attribute set to `internal` or `leaf`.
A module has a `GeneTree` which contains a tree structure of `Child` elements, either with `node` attribute set to `internal` or `leaf`. Multiple `leaf` children should be bundled into an `internal` child.
Each child has an ordered set of `Gene` elements. A gene has a `name` attribute and an optional `alias` (symbolic name). Symbolic names could also be loaded from a simple mapping file at a later stage.
Regulator data is formatted in a similar way, but uses `RegulatorTree` elements instead of `GeneTree`.
