PADRE: a package for analyzing and displaying reticulate evolution

Lott, Martin; Spillner, Andreas; Huber, Katharina T.; Moulton, Vincent

doi:10.1093/bioinformatics/btp133

Cited by 37 publications

(34 citation statements)

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“…The goal of the algorithm is to construct a minimal MUL tree that is consistent with the input set of triplets and minimizes the number of its duplications. Note that a phylogenetic network can be associated to a MUL tree [14]. Therefore, it seems that constructing the smallest MUL tree from a set of triplets could be an alternative method for the problem of constructing a phylogenetic network with minimum reticulation from a set of triplets.…”

Section: Discussion and Future Workmentioning

confidence: 99%

“…Several algorithms for constructing MUL trees from various datasets are introduced. Examples include building consensus MUL trees [6], [14], [15], constructing a phylogenetic network from a MUL tree [10] and transforming a collection of MUL trees into a collection of evolutionary trees [23]. One of the problems in the field of inferring MUL trees is to construct a smallest possible MUL tree consistent with a given set of rooted triplets, or SMRT problem for short.…”

Section: Introductionmentioning

confidence: 99%

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Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

2014

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The evolutionary history of certain species such as polyploids are modeled by a generalization of phylogenetic trees called multi-labeled phylogenetic trees, or MUL trees for short. One problem that relates to inferring a MUL tree is how to construct the smallest possible MUL tree that is consistent with a given set of rooted triplets, or SMRT problem for short. This problem is NP-hard. There is one algorithm for the SMRT problem which is exact and runs in time, where is the number of taxa. In this paper, we show that the SMRT does not seem to be an appropriate solution from the biological point of view. Indeed, we present a heuristic algorithm named MTRT for this problem and execute it on some real and simulated datasets. The results of MTRT show that triplets alone cannot provide enough information to infer the true MUL tree. So, it is inappropriate to infer a MUL tree using triplet information alone and considering the minimum number of duplications. Finally, we introduce some new problems which are more suitable from the biological point of view.

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Section: Discussion and Future Workmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

2014

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“…In addition to tree nodes —nodes with only one parent—, they allow hybrid nodes —nodes with two parents. Thus, phylogenetic networks are more expressive than phylogenetic trees [29,30]. In the same way that agreement trees and majority rule trees extract consensus information in phylogenetic trees, consensus networks [31] represent frequent patterns in phylogenetic networks [32].…”

Section: Introductionmentioning

confidence: 99%

Enumerating all maximal frequent subtrees in collections of phylogenetic trees

Deepak

Fernández-Baca

2014

Algorithms Mol Biol

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BackgroundA common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events.ResultsWe give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/.ConclusionsOur computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees.

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“…Here, the input is a collection of gene trees where the same species name can label more than one leaf (i.e., MUL-trees), and the output should be a leaf-labeled directed acyclic graph called a phylogenetic network, in which each species name appears once only. Lott et al (2009a) suggested that rather than inferring a phylogenetic network directly, it may be easier to first reconcile the input into a single MUL-tree and then apply an algorithm from Huber et al (2006) that is guaranteed to output a network with the minimum number of non tree nodes. For this purpose, Lott et al (2009b) presented a method for constructing a greedy kind of consensus MUL-tree that uses the same basic strategy as the well-known greedy consensus tree method (Bryant, 2003;Sung, 2010) for single-labeled phylogenetic trees.…”

Section: Introductionmentioning

confidence: 99%

“…For this purpose, Lott et al (2009b) presented a method for constructing a greedy kind of consensus MUL-tree that uses the same basic strategy as the well-known greedy consensus tree method (Bryant, 2003;Sung, 2010) for single-labeled phylogenetic trees. A serious disadvantage of their method is that its running time is exponential in the size of the input, and indeed, according to the discussion in Lott et al (2009a), the method probably needs to be improved to deal with datasets from new sequencing technologies in the near future. A recent article (Huber et al, 2012) incorporates a fixed-parameter algorithm from Section 5 of Huber et al (2008) to obtain a faster and more practical method for building a greedy consensus MUL-tree, but its worst-case running time remains exponential.…”

Section: Introductionmentioning

confidence: 99%

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

Cui

Jansson

Sung

2012

Journal of Computational Biology

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A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host-parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists.

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PADRE: a package for analyzing and displaying reticulate evolution

Abstract: PADRE is an open-source Java program freely available from http://www.uea.ac.uk/cmp/research/cmpbio/PADRE.

Cited by 37 publications

References 7 publications

Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

Do Triplets Have Enough Information to Construct the Multi-Labeled Phylogenetic Tree?

Enumerating all maximal frequent subtrees in collections of phylogenetic trees

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

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