Who is Who in Phylogenetic Networks

Publications list	Showing 391 - 420 (752 total)

391 Leo van Iersel, Charles Semple and Mike Steel. Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'. In BMB, Vol. 72:1783–1798, 2010. Note: http://www.win.tue.nl/~liersel/LGT.pdf.         Toggle abstract "The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss, and lateral gene transfer (LGT). The extent of LGT, particularly in prokaryotes, and its implications for creating a 'network of life' rather than a 'tree of life' is controversial. In this paper, we formally model the problem of quantifying LGT, and provide exact mathematical bounds, and new computational results. In particular, we investigate the computational complexity of quantifying the extent of LGT under the simple models of gene genesis, loss, and transfer on which a recent heuristic analysis of biological data relied. Our approach takes advantage of a relationship between LGT optimization and graph-theoretical concepts such as tree width and network flow. © 2010 Society for Mathematical Biology." 392 Miguel Arenas, Mateus Patricio, David Posada and Gabriel Valiente. Characterization of Phylogenetic Networks with NetTest. In BMCB, Vol. 11:268, 2010. Keywords: explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree sibling network, tree-child network, visualization. Note: http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/.         Toggle abstract "Background: Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions that will likely not be met by the evolutionary process. We have recently shown that the complexity of simulated networks is a function of the population recombination rate, and that at moderate and large recombination rates the resulting networks cannot be categorized. However, we do not know whether these results extend to networks estimated from real data.Results: We introduce a web server for the categorization of explicit phylogenetic networks, including the most relevant theoretical classes developed so far. Using this tool, we analyzed statistical parsimony phylogenetic networks estimated from ~5,000 DNA alignments, obtained from the NCBI PopSet and Polymorphix databases. The level of characterization was correlated to nucleotide diversity, and a high proportion of the networks derived from these data sets could be formally characterized.Conclusions: We have developed a public web server, NetTest (freely available from the software section at http://darwin.uvigo.es), to formally characterize the complexity of phylogenetic networks. Using NetTest we found that most statistical parsimony networks estimated with the program TCS could be assigned to a known network class. The level of network characterization was correlated to nucleotide diversity and dependent upon the intra/interspecific levels, although no significant differences were detected among genes. More research on the properties of phylogenetic networks is clearly needed. © 2010 Arenas et al; licensee BioMed Central Ltd." 393 Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010. Keywords: agreement forest, explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software. Note: http://www.biomedcentral.com/1471-2105/11/324.         Toggle abstract "Background: To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.Results: We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.Conclusions: The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier. © 2010 Abby et al; licensee BioMed Central Ltd." 394 Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010. Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network. Note: http://dx.doi.org/10.1186/1471-2148-10-254.         Toggle abstract "Background. A phylogenetic network is a generalization of phylogenetic trees that allows the representation of conflicting signals or alternative evolutionary histories in a single diagram. There are several methods for constructing these networks. Some of these methods are based on distances among taxa. In practice, the methods which are based on distance perform faster in comparison with other methods. The Neighbor-Net (N-Net) is a distance-based method. The N-Net produces a circular ordering from a distance matrix, then constructs a collection of weighted splits using circular ordering. The SplitsTree which is a program using these weighted splits makes a phylogenetic network. In general, finding an optimal circular ordering is an NP-hard problem. The N-Net is a heuristic algorithm to find the optimal circular ordering which is based on neighbor-joining algorithm. Results. In this paper, we present a heuristic algorithm to find an optimal circular ordering based on the Monte-Carlo method, called MC-Net algorithm. In order to show that MC-Net performs better than N-Net, we apply both algorithms on different data sets. Then we draw phylogenetic networks corresponding to outputs of these algorithms using SplitsTree and compare the results. Conclusions. We find that the circular ordering produced by the MC-Net is closer to optimal circular ordering than the N-Net. Furthermore, the networks corresponding to outputs of MC-Net made by SplitsTree are simpler than N-Net. © 2010 Eslahchi et al; licensee BioMed Central Ltd." 395 Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010. Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction. Note: http://dx.doi.org/10.1186/1471-2148-10-131.         Toggle abstract "Background. Maximum parsimony is one of the most commonly used criteria for reconstructing phylogenetic trees. Recently, Nakhleh and co-workers extended this criterion to enable reconstruction of phylogenetic networks, and demonstrated its application to detecting reticulate evolutionary relationships. However, one of the major problems with this extension has been that it favors more complex evolutionary relationships over simpler ones, thus having the potential for overestimating the amount of reticulation in the data. An ad hoc solution to this problem that has been used entails inspecting the improvement in the parsimony length as more reticulation events are added to the model, and stopping when the improvement is below a certain threshold. Results. In this paper, we address this problem in a more systematic way, by proposing a nonparametric bootstrap-based measure of support of inferred reticulation events, and using it to determine the number of those events, as well as their placements. A number of samples is generated from the given sequence alignment, and reticulation events are inferred based on each sample. Finally, the support of each reticulation event is quantified based on the inferences made over all samples. Conclusions. We have implemented our method in the NEPAL software tool (available publicly at http://bioinfo.cs.rice.edu/), and studied its performance on both biological and simulated data sets. While our studies show very promising results, they also highlight issues that are inherently challenging when applying the maximum parsimony criterion to detect reticulate evolution. © 2010 Park et al; licensee BioMed Central Ltd." 396 Pawel Górecki. H-trees: a model of evolutionary scenario with horizontal gene transfer. In Fundamenta Informaticae, Vol. 103:105-128, 2010. Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, uniqueness.         397 Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Path lengths in tree-child time consistent hybridization networks. In Information Sciences, Vol. 180(3):366-383, 2010. Keywords: distance between networks, phylogenetic network, phylogeny, time consistent network, tree-child network. Note: http://arxiv.org/abs/0807.0087?context=cs.CE.         Toggle abstract "Hybridization networks are representations of evolutionary histories that allow for the inclusion of reticulate events like recombinations, hybridizations, or lateral gene transfers. The recent growth in the number of hybridization network reconstruction algorithms has led to an increasing interest in the definition of metrics for their comparison that can be used to assess the accuracy or robustness of these methods. In this paper we establish some basic results that make it possible the generalization to tree-child time consistent (TCTC) hybridization networks of some of the oldest known metrics for phylogenetic trees: those based on the comparison of the vectors of path lengths between leaves. More specifically, we associate to each hybridization network a suitably defined vector of 'splitted' path lengths between its leaves, and we prove that if two TCTC hybridization networks have the same such vectors, then they must be isomorphic. Thus, comparing these vectors by means of a metric for real-valued vectors defines a metric for TCTC hybridization networks. We also consider the case of fully resolved hybridization networks, where we prove that simpler, 'non-splitted' vectors can be used. © 2009 Elsevier Inc. All rights reserved." 398 Johannes Fischer and Daniel H. Huson. New Common Ancestor Problems in Trees and Directed Acyclic Graphs. In IPL, Vol. 110(8-9):331-335, 2010. Keywords: explicit network, phylogenetic network, polynomial. Note: http://www-ab.informatik.uni-tuebingen.de/people/fischer/lsa.pdf.         Toggle abstract "We derive a new generalization of lowest common ancestors (LCAs) in dags, called the lowest single common ancestor (LSCA). We show how to preprocess a static dag in linear time such that subsequent LSCA-queries can be answered in constant time. The size is linear in the number of nodes. We also consider a "fuzzy" variant of LSCA that allows to compute a node that is only an LSCA of a given percentage of the query nodes. The space and construction time of our scheme for fuzzy LSCAs is linear, whereas the query time has a sub-logarithmic slow-down. This "fuzzy" algorithm is also applicable to LCAs in trees, with the same complexities. © 2010 Elsevier B.V. All rights reserved." 399 Leo van Iersel, Charles Semple and Mike Steel. Locating a tree in a phylogenetic network. In IPL, Vol. 110(23), 2010. Keywords: cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree containment, tree sibling network, tree-child network. Note: http://arxiv.org/abs/1006.3122.         Toggle abstract "Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a cluster of some phylogenetic tree embedded in the network. Both problems are known to be NP-complete in general. In this article, we consider the restriction of these problems to several well-studied classes of phylogenetic networks. We show that Tree Containment is polynomial-time solvable for normal networks, for binary tree-child networks, and for level-k networks. On the other hand, we show that, even for tree-sibling, time-consistent, regular networks, both Tree Containment and Cluster Containment remain NP-complete. © 2010 Elsevier B.V. All rights reserved." 400 Frederick A. Matsen. ConstNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints. In JCB, Vol. 17(6):799-818, 2010. Keywords: from distances, Program constNJ, reconstruction. Note: http://arxiv.org/abs/0901.1598v2.         Toggle abstract "This article introduces constNJ (constrained neighbor-joining), an algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune-regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees that must fit into a recombination, hybridization, or similar network. Rather than first finding a set of trees that are optimal according to a phylogenetic criterion (e.g., likelihood or parsimony) and then attempting to fit them into a network, constNJ estimates the trees while enforcing specified rSPR distance constraints. The primary input for constNJ is a collection of distance matrices derived from sequence blocks which are assumed to have evolved in a tree-like manner, such as blocks of an alignment which do not contain any recombination breakpoints. The other input is a set of rSPR constraint inequalities for any set of pairs of trees. constNJ is consistent and a strict generalization of the neighbor-joining algorithm; it uses the new notion of maximum agreement partitions (MAPs) to assure that the resulting trees satisfy the given rSPR distance constraints. Copyright 2010, Mary Ann Liebert, Inc." 401 Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010. Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction. Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.         402 Sagi Snir and Edward Trifonov. A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. In JCB, Vol. 17(11):1535-1548, 2010. Keywords: from sequences, phylogenetic network, phylogeny, reconstruction. Note: http://research.haifa.ac.il/~ssagi/published%20papers/JCB-HGT.pdf.         Toggle abstract "Horizontal transfer (HT) is the event of a DNA sequence being transferred between species not by inheritance. This phenomenon violates the tree-like evolution of the species under study turning the trees into networks. At the sequence level, HT offers basic characteristics that enable not only clear identification and distinguishing from other sequence similarity cases but also the possibility of dating the events. We developed a novel, self-contained technique to identify relatively recent horizontal transfer elements (HTEs) in the sequences. Appropriate formalism allows one to obtain confidence values for the events detected. The technique does not rely on such problematic prerequisites as reliable phylogeny and/or statistically justified pairwise sequence alignment. In conjunction with the unique properties of HT, it gives rise to a two-level sequence similarity algorithm that, to the best of our knowledge, has not been explored. From evolutionary perspective, the novelty of the work is in the combination of small scale and large scale mutational events. The technique is employed on both simulated and real biological data. The simulation results show high capability of discriminating between HT and conserved regions. On the biological data, the method detected documented HTEs along with their exact locations in the recipient genomes. Supplementary Material is available online at www.libertonline.com/cmb. Copyright 2010, Mary Ann Liebert, Inc." 403 Simone Linz, Charles Semple and Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715-737, 2010. Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network. Note: http://dx.doi.org/10.1007/s00285-009-0319-y..         Toggle abstract "Reticulation networks are now frequently used to model the history of life for various groups of species whose evolutionary past is likely to include reticulation events such as horizontal gene transfer or hybridization. However, the reconstructed networks are rarely guaranteed to be temporal. If a reticulation network is temporal, then it satisfies the two biologically motivated timing constraints of instantaneously occurring reticulation events and successively occurring speciation events. On the other hand, if a reticulation network is not temporal, it is always possible to make it temporal by adding a number of additional unsampled or extinct taxa. In the first half of the paper, we show that deciding whether a given number of additional taxa is sufficient to transform a non-temporal reticulation network into a temporal one is an NP-complete problem. As one is often given a set of gene trees instead of a network in the context of hybridization, this motivates the second half of the paper which provides an algorithm, called TemporalHybrid, for reconstructing a temporal hybridization network that simultaneously explains the ancestral history of two trees or indicates that no such network exists. We further derive two methods to decide whether or not a temporal hybridization network exists for two given trees and illustrate one of the methods on a grass data set. © 2009 The Author(s)." 404 Jaroslaw Byrka, Pawel Gawrychowski, Katharina Huber and Steven Kelk. Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):65-75, 2010. Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/0710.3258.         Toggle abstract "The study of phylogenetic networks is of great interest to computational evolutionary biology and numerous different types of such structures are known. This article addresses the following question concerning rooted versions of phylogenetic networks. What is the maximum value of p ∈ [0, 1] such that for every input set T of rooted triplets, there exists some network N such that at least p | T | of the triplets are consistent with N? We call an algorithm that computes such a network (where p is maximum) worst-case optimal. Here we prove that the set containing all triplets (the full triplet set) in some sense defines p. Moreover, given a network N that obtains a fraction p′ for the full triplet set (for any p′), we show how to efficiently modify N to obtain a fraction ≥ p′ for any given triplet set T. We demonstrate the power of this insight by presenting a worst-case optimal result for level-1 phylogenetic networks improving considerably upon the 5/12 fraction obtained recently by Jansson, Nguyen and Sung. For level-2 phylogenetic networks we show that p ≥ 0.61. We emphasize that, because we are taking | T | as a (trivial) upper bound on the size of an optimal solution for each specific input T, the results in this article do not exclude the existence of approximation algorithms that achieve approximation ratio better than p. Finally, we note that all the results in this article also apply to weighted triplet sets. © 2009 Elsevier B.V. All rights reserved." 405 David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010. Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition. Note: http://dx.doi.org/10.1093/molbev/msp309.         Toggle abstract "Exploratory data analysis (EDA) is a frequently undervalued part of data analysis in biology. It involves evaluating the characteristics of the data "before" proceeding to the definitive analysis in relation to the scientific question at hand. For phylogenetic analyses, a useful tool for EDA is a data-display network. This type of network is designed to display any character (or tree) conflict in a data set, without prior assumptions about the causes of those conflicts. The conflicts might be caused by 1) methodological issues in data collection or analysis, 2) homoplasy, or 3) horizontal gene flow of some sort. Here, I explore 13 published data sets using splits networks, as examples of using data-display networks for EDA. In each case, I performed an original EDA on the data provided, to highlight the aspects of the resulting network that will be important for an interpretation of the phylogeny. In each case, there is at least one important point (possibly missed by the original authors) that might affect the phylogenetic analysis. I conclude that EDA should play a greater role in phylogenetic analyses than it has done. © 2010 The Author. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved." 406 Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola and Lusheng Wang. Beyond evolutionary trees. In Natural Computing, Vol. 9(2):421-435, 2010. Note: http://dx.doi.org/10.1007/s11047-009-9156-6.         Toggle abstract "In Computational Biology, the notion of phylogeny has become synonymous with tree-like evolution. Recent advances in the Life Sciences have suggested that evolution has a much more diverse course. In this paper we will survey some of the models that have been proposed to overcome the limitations of using phylogenies to represent evolutionary histories. © 2009 Springer Science+Business Media B.V." 407 Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010.1-13, 2010. Keywords: explicit network, from sequences, phylogenetic network, phylogeny. Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.         Toggle abstract "Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have finetuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation. © 2010 Mele ́ et al." 408 Alix Boc, Hervé Philippe and Vladimir Makarenkov. Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. In Systematic Biology, Vol. 59(2):195-211, 2010. Note: http://www.info2.uqam.ca/~makarenv/makarenv/Artcile_SB_2010.pdf.         409 Erik W. Bloomquist and Marc A. Suchard. Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework. In Systematic Biology, Vol. 59(1):27-41, 2010. Note: http://dx.doi.org/10.1093/sysbio/syp076.         410 Luay Nakhleh. A Metric on the Space of Reduced Phylogenetic Networks. In TCBB, Vol. 7(2), 2010. Keywords: distance between networks, phylogenetic network, phylogeny. Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-Metric.pdf.         Toggle abstract "Phylogenetic networks are leaf-labeled, rooted, acyclic, and directed graphs that are used to model reticulate evolutionary histories. Several measures for quantifying the topological dissimilarity between two phylogenetic networks have been devised, each of which was proven to be a metric on certain restricted classes of phylogenetic networks. A biologically motivated class of phylogenetic networks, namely, reduced phylogenetic networks, was recently introduced. None of the existing measures is a metric on the space of reduced phylogenetic networks. In this paper, we provide a metric on the space of reduced phylogenetic networks that is computable in time polynomial in the size of the networks. © 2006 IEEE." 411 Stephen J. Willson. Regular Networks Can Be Uniquely Constructed from Their Trees. In TCBB, Vol. 8(3):785-796, 2010. Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, regular network. Note: http://www.public.iastate.edu/~swillson/RegularNetsFromTrees5.pdf.         Toggle abstract "A rooted acyclic digraph N with labeled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general, there may be many other networks M, such that Tr(M) = Tr(N). A network is regular if it is isomorphic with its cover digraph. If N is regular and D is a collection of trees displayed by N, this paper studies some procedures to try to reconstruct N given D. If the input is D=Tr(N), one procedure is described, which will reconstruct N. Hence, if N and M are regular networks and Tr(N) = Tr(M), it follows that N = M, proving that a regular network is uniquely determined by its displayed trees. If D is a (usually very much smaller) collection of displayed trees that satisfies certain hypotheses, modifications of the procedure will still reconstruct N given D. © 2011 IEEE." 412 Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009. Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction. Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.         413 Martin Lott. New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees. PhD thesis, University of East Anglia, U.K., 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://www.ic0.net/thesis-martin-final.pdf.         414 Klaus Schliep. Some applications of statistical phylogenetics. PhD thesis, Massey University, New Zealand, 2009. Keywords: abstract network, phylogenetic network, Program Phangorn, reconstruction, split network. Note: http://muir.massey.ac.nz/handle/10179/931.         415 Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009. Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software. Note: http://hdl.handle.net/10092/2852.         416 Ali Tofigh. Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden, 2009. Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction. Note: http://kth.diva-portal.org/smash/record.jsf?pid=diva2:220830&searchId=1.         417 Ali Tofigh, Joel Sjöstrand, Bengt Sennblad, Lars Arvestad and Jens Lagergren. Detecting LGTs using a novel probabilistic model integrating duplications, LGTs, losses, rate variation, and sequence evolution. 2009. Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction. Note: http://kth.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:233574.         418 Leo van Iersel and Steven Kelk. A short note on the tractability of constructing phylogenetic networks from clusters. 2009. Keywords: from clusters, from triplets, level k phylogenetic network, phylogenetic network, polynomial, reconstruction. Note: http://arxiv.org/abs/0912.4502.         419 Gabriel Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R. Pages 184-208, Taylor & Francis/CRC Press, 2009. Keywords: counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree sibling network, tree-child network. Note: http://books.google.fr/books?id=F4YIIUWb7yMC.         420 Qiong Wu. Phylogenetic Networks: New Constructions and Applications. PhD thesis, Université of East Anglia, U.K., 2009. Keywords: abstract network, phylogenetic network, phylogeny, reconstruction, split network. Note: http://ethos.bl.uk/OrderDetails.do?did=1&uin=uk.bl.ethos.514315.