So I am using http://bl.ocks.org/mbostock/4339083 to create a collapsible tree and it works great.
Now the thing is I have some nodes which have the same children, s
From your description, I gather you need to visualize directed acyclic graph, or DAG.
Tree is:
A
|\
B C
/ \
D E
DAG is:
A
|\
B C
\|
D
And, no, unfortunately, D3 tree and cluster layouts simply don't support that kind of graphs. Their internal algorithms assume that the data structure is strictly a tree.
However, there are some options. Please see these five related questions for possible approaches:
d3 tree - parents having same children
How to layout a non-tree hierarchy with D3
d3.js tree nodes with same parents
Layered graphs in d3.js
JS library for displaying direct acyclic graphs (DAGs)