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A practical algorithm for reconstructing level1 phylogenetic networks
 IEEE/ACM Transactions on Computational Biology and Bioinformatics
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QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS
, 2012
"... Accepted (Day Month Year) Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogen ..."
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Accepted (Day Month Year) Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analogue of levelk networks. In particular, we give an equivalence theorem between circular split systems and unrooted level1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted levelk phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.
RESEARCH Open Access
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First somatic mutation of E2F1 in a critical DNA binding residue discovered in welldifferentiated papillary mesothelioma of the peritoneum
RECONSTRUCTING PHYLOGENETIC LEVEL1 NETWORKS FROM NONDENSE BINET AND TRINET SETS
"... Abstract. Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level1 phylogenetic network displaying a given set T of binary binets or trinets over a taxa set X, and constructing such a network whene ..."
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Abstract. Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level1 phylogenetic network displaying a given set T of binary binets or trinets over a taxa set X, and constructing such a network whenever it exists. We show that this is NPhard for trinets but polynomialtime solvable for binets. Moreover, we show that the problem is still polynomialtime solvable for inputs consisting of binets and trinets as long as the cycles in the trinets have size three. Finally, we present an O(3Xpoly(X)) time algorithm for general sets of binets and trinets. The latter two algorithms generalise to instances containing level1 networks with arbitrarily many leaves, and thus provide some of the first supernetwork algorithms for computing networks from a set of rooted phylogenetic networks. 1.
A practical algorithm for reconstructing . . .
, 2010
"... Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level1 phylogenetic networks a type of network slig ..."
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Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level1 phylogenetic networks a type of network slightly more general than a phylogenetic tree from triplets. Our algorithm has been made publicly available as the program LEV1ATHAN. It combines ideas from several known theoretical algorithms for phylogenetic tree and network reconstruction with two novel subroutines. Namely, an exponentialtime exact and a greedy algorithm both of which are of independent theoretical interest. Most importantly, LEV1ATHAN runs in polynomial time and always constructs a level1 network. If the data are consistent with a phylogenetic tree, then the algorithm constructs such a tree. Moreover, if the input triplet set is dense and, in addition, is fully consistent with some level1 network, it will find such a network. The potential of LEV1ATHAN is explored by means of an extensive simulation study and a biological data set. One of our conclusions is that LEV1ATHAN is able to construct networks consistent with a high percentage of input triplets, even when these input triplets are affected by a low to moderate level of noise.
TRINETS ENCODE TREECHILD AND LEVEL2 PHYLOGENETIC NETWORKS
"... Abstract. Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to dev ..."
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Abstract. Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to develop methods to construct rooted phylogenetic networks from triplets, that is rooted trees on three species. However, although triplets determine or encode rooted phylogenetic trees, they do not in general encode rooted phylogenetic networks, which is a potential issue for any such method. Motivated by this fact, Huber and Moulton recently introduced trinets as a natural extension of rooted triplets to networks. In particular, they showed that level1 phylogenetic networks are encoded by their trinets, and also conjectured that all “recoverable ” rooted phylogenetic networks are encoded by their trinets. Here we prove that recoverable binary level2 networks and binary treechild networks are also encoded by their trinets. To do this we prove two decomposition theorems based on trinets which hold for all recoverable binary rooted phylogenetic networks. Our results provide some additional evidence in support of the conjecture that trinets encode all recoverable rooted phylogenetic networks, and could also lead to new approaches to construct phylogenetic networks from trinets. 1.
Advance Access publication September 18, 2014 How Much Information is Needed to Infer Reticulate Evolutionary Histories?
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which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.