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Why does layout for selection takes very long time?

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I am using yEd to give a graphical overview of a genealogy database. Applying hieararchical layout to the whole graph produces a layout with LOTS of overlapping edges. Therefore I am applying layout on a selection and then ordering the selections manually. Applying layout on some 30-40 nodes out of the total 4000 takes several minutes compared to applying hierarchical layout to a complete much smaller graph of only 30-40 nodes which is quite quick. Why is this?
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