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Tanglegrams for rooted phylogenetic trees and networks.

Scornavacca C, Zickmann F, Huson DH - Bioinformatics (2011)

Bottom Line: We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets.For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org. scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany. scornava@informatik.uni-tuebingen.de

ABSTRACT

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks.

Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.

Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.

Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de.

Show MeSH
(a) A phylogenetic network N. (b) A concrete drawing τ of the forest ℱ(N). This drawing induces a partial order of the leaves such that a<τd<τf<τg<τh<τl, i<τj<τk, and b<τc.
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Figure 3: (a) A phylogenetic network N. (b) A concrete drawing τ of the forest ℱ(N). This drawing induces a partial order of the leaves such that a<τd<τf<τg<τh<τl, i<τj<τk, and b<τc.

Mentions: For example, for the phylogenetic network N on 𝒳={a,…,l} and the concrete drawing θ of the forest ℱ(N) in Figure 3, both (a,b,c,d,e,f,g,h,i,j,k,l) and (a,d,f,g,h,l,i,j,k,b,c,e) are non-interleaving total orders on 𝒳 w.r.t. θ, while (a,d,f,g,h,i,j,l,k,b,c,e) is not because it violates condition (2) of Definition 3.1.Fig. 3.


Tanglegrams for rooted phylogenetic trees and networks.

Scornavacca C, Zickmann F, Huson DH - Bioinformatics (2011)

(a) A phylogenetic network N. (b) A concrete drawing τ of the forest ℱ(N). This drawing induces a partial order of the leaves such that a<τd<τf<τg<τh<τl, i<τj<τk, and b<τc.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3117342&req=5

Figure 3: (a) A phylogenetic network N. (b) A concrete drawing τ of the forest ℱ(N). This drawing induces a partial order of the leaves such that a<τd<τf<τg<τh<τl, i<τj<τk, and b<τc.
Mentions: For example, for the phylogenetic network N on 𝒳={a,…,l} and the concrete drawing θ of the forest ℱ(N) in Figure 3, both (a,b,c,d,e,f,g,h,i,j,k,l) and (a,d,f,g,h,l,i,j,k,b,c,e) are non-interleaving total orders on 𝒳 w.r.t. θ, while (a,d,f,g,h,i,j,l,k,b,c,e) is not because it violates condition (2) of Definition 3.1.Fig. 3.

Bottom Line: We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets.For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org. scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany. scornava@informatik.uni-tuebingen.de

ABSTRACT

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks.

Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.

Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.

Contact: scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de.

Show MeSH