A navigation system for tree space

Mark, Sarah; McLeod, Jeanette C.; Steel, Mike

doi:10.7155/jgaa.00392

Cited by 4 publications

(4 citation statements)

References 5 publications

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“…For instance, it may help studying how trees from the same stand and also between different stands are connected via common topological rearrangements (e.g. Nearest Neighbour Interchange, see also ( 32 )), which has a great potential for development of better tree search strategies in the presence of missing data. Note, that for supertree methods distinct trees can have identical score even without missing data ( 5, 33 ).…”

Section: Discussionmentioning

confidence: 99%

“…For instance, it allows investigating scoring landscapes imposed by missing data as well as studying how trees from the same stand and also between different stands are connected via common topological rearrangements (e.g. Nearest Neighbour Interchange, see also 30 ). This knowledge has a great potential for development of better tree search strategies in the presence of missing data 9,10 .…”

Section: Discussionmentioning

confidence: 99%

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Gentrius: identifying equally scoring trees in phylogenomics with incomplete data

Chernomor

Elgert

Haeseler

2023

Preprint

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Phylogenetic trees are routinely built from huge and yet incomplete multi-locus datasets often leading to multiple equally scoring trees under many common criteria. As typical tree inference software output only a single tree, identifying all trees with identical score challenges phylogenomics. Here, we introduce Gentrius, an efficient algorithm that tackles this problem. We showed on simulated and biological datasets that Gentrius generates millions of trees within seconds. Depending on the distribution of missing data across species and loci and the inferred phylogeny, the number of equally good trees varies tremendously. The strict consensus tree computed from them displays all the branches unaffected by the pattern of missing data. Thus, Gentrius provides an important systematic assessment of phylogenetic trees inferred from incomplete data.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Gentrius: identifying equally scoring trees in phylogenomics with incomplete data

Chernomor

Elgert

Haeseler

2023

Preprint

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“…Bordewich [Bor03, Proposition 2.9] and Mark et al [MMS16] showed that the space of rooted phylogenetic trees that display a set of triplets (trees on three leaves) is connected under NNI. Furthermore, Bordewich et al [BLS17] showed that the space of rooted phylogenetic networks that display a set of rooted phylogenetic trees is connected.…”

Section: Network Displaying Networkmentioning

confidence: 99%

Rearrangement operations on unrooted phylogenetic networks

Janssen¹,

Klawitter²

2019

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Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree prune and regraft), and TBR (tree bisection and reconnection). Recently, these operations have been extended to unrooted phylogenetic networks, which are generalisations of phylogenetic trees that can model reticulated evolutionary relationships.Here, we study global and local properties of spaces of phylogenetic networks under these three operations. In particular, we prove connectedness and asymptotic bounds on the diameters of spaces of different classes of phylogenetic networks, including tree-based and level-k networks. We also examine the behaviour of shortest TBR-sequence between two phylogenetic networks in a class, and whether the TBR-distance changes if intermediate networks from other classes are allowed: for example, the space of phylogenetic trees is an isometric subgraph of the space of phylogenetic networks under TBR. Lastly, we show that computing the TBR-distance and the PR-distance of two phylogenetic networks is NP-hard.

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“…According to [1], let T ∈ RB(X) and let e = (v, u) be an arc of T. We say that T 1 ∈ RB(X) is an rSPR-neighbour of T if T 1 can be obtained from T by the following procedure. Let t u be the subtree of T rooted at u. Delete arc e, pruning the subtree t u .…”

Section: Rooted Subtree Pruned and Regraft (Rspr)mentioning

confidence: 99%

Survey on Plane 3-Tree with Nearest Neighbor Interchanges and Chordal Bipartite Graph

Afroze¹

2017

IJCA

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Graph theory is an ancient branch of engineering. Many problems of real-world have been solved by graph theory's principles. In this survey paper, I want to present the plane 3-tree's concept with an interesting branch of another topic of graph theory, that is, chordal bipartite graph. Throughout the development of this survey paper, we will present definitions of chordal graph, bipartite graph, tree, plane 3-tree and different operations of tree architecture. Then I will show a new way to look at the tree architecture with nearest neighbor interchanges. Nearest Neighbor Interchanges is a mechanism that deals with the operation of relative nodes in a tree architecture. Relative nodes are those nodes which come in a same branch or in different branch of a tree which do not interrupt the way from leaf to root with other nodes in the same branch or in another branch are used in the nearest neighbor interchanges to interchange or exchange.We have many applications in which we can apply this nearest neighbor interchange mechanism. The main application is in DNA matching, DNA synthesizing and ribosome particles analysis. I will clearly describe these features in detail in the specified sections of this survey paper. Next I want to show that plane 3-tree has passed the planarity criteria, that is, plane 3-tree is a planar graph and it has straight-line drawing. So, we can construct a bipartite, chordal and chordal bipartite graph which is relevant with the given plane 3-tree. The novelty of this survey paper comprised of several definitions, graphical illustrations of different graph operations and chordal bipartite equivalent of a plane 3-tree.

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A navigation system for tree space

Cited by 4 publications

References 5 publications

Gentrius: identifying equally scoring trees in phylogenomics with incomplete data

Gentrius: identifying equally scoring trees in phylogenomics with incomplete data

Rearrangement operations on unrooted phylogenetic networks

Survey on Plane 3-Tree with Nearest Neighbor Interchanges and Chordal Bipartite Graph

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