Geodesic
Efficient drawing of RNA secondary structure
Journal of Graph Algorithms and Applications, Tome 10 (2006) no. 2, pp. 329-351.

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In this paper, we propose a new layout algorithm that draws the secondary structure of a Ribonucleic Acid (RNA) automatically according to some of the biologists' aesthetic criteria. Such layout insures that two equivalent structures (or sub-structures) are drawn in a same and planar way. In order to allow a visual comparison of two RNAs, we use an heuristic that places the biggest similar part of the two structures in the same position and orientation. 
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     author = {David Auber and Maylis Delest and Jean-Philippe Domenger and Serge Dulucq},
     title = {Efficient drawing of {RNA} secondary structure},
     journal = {Journal of Graph Algorithms and Applications},
     pages = {329--351},
     publisher = {mathdoc},
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     doi = {10.7155/jgaa.00131},
     language = {en},
     url = {http://geodesic.mathdoc.fr/articles/10.7155/jgaa.00131/}
}
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David Auber; Maylis Delest; Jean-Philippe Domenger; Serge Dulucq. Efficient drawing of RNA secondary structure. Journal of Graph Algorithms and Applications, Tome 10 (2006) no. 2, pp. 329-351. doi : 10.7155/jgaa.00131. http://geodesic.mathdoc.fr/articles/10.7155/jgaa.00131/

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