Steiner Tree Implementations

Question

[Sudeep]

Hi all,

I am looking for Steiner tree implementations that can take an edge weighted/un-weighted (ppi) graph as an input. So far I found 4 implementations of Steiner trees in bioinformatics BioNet, MSGSTEINER, GenRev and SteinerNet, so my question is do you know any other well known implementations of Steiner trees in bioinformatic/ non bioinformatic field ? any suggestions ?

Thank you.

Answer 1

[Woa]

I too was looking for PC Steiner Tree's implementations in recent time. The following paper used a heuristic steiner tree as implemented using the "Goblin" package. http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200482/full

The URL mentioned in the paper is down, but was active at least a couple of months ago, when I downloaded it.Anyway you can download it from the cached page: http://web.archive.org/web/20120127034345/http://www.math.uni-augsburg.de/~fremuth/goblin.html

There is an web version too: http://fraenkel.mit.edu/steinernet/

Check also a recent paper by Fraenkel and Tuncbag in Journal of Computational Biology

[Sudeep]

Thanks, I too came across steinernet while looking around, I avoided it because it's available just as a web version, but I never came across Goblin though.

[Woa]

Besides, as ST is a classic graph theory problem, I guess codes in C/C++ must be lying here and there. The "Boost" graph library may be having it. I didn't find any python lib. in first glance but GenRev is coded in python I guess.