Search Results - "Warnow, T"

ASTRAL: genome-scale coalescent-based species tree estimation by Mirarab, S, Reaz, R, Bayzid, Md S, Zimmermann, T, Swenson, M S, Warnow, T

“…Species trees provide insight into basic biology, including the mechanisms of evolution and how it modifies biomolecular function and structure, biodiversity…”
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SEPP: SATé-enabled phylogenetic placement by Mirarab, S, Nguyen, N, Warnow, T

“…We address the problem of Phylogenetic Placement, in which the objective is to insert short molecular sequences (called query sequences) into an existing…”
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Inferring optimal species trees under gene duplication and loss by Bayzid, M S, Mirarab, S, Warnow, T

“…Species tree estimation from multiple markers is complicated by the fact that gene trees can differ from each other (and from the true species tree) due to…”
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Phylogenetic networks: modeling, reconstructibility, and accuracy by Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., Timme, R.

“…Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of…”
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Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy by Liu, K., Nelesen, S., Raghavan, S., Linder, C.R., Warnow, T.

“…The current technique for estimating phylogenies from sequence data uses two phases: first, the sequences are aligned, and then the tree is estimated using the…”
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Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology by HENZINGER, M. R, KING, V, WARNOW, T

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Pattern Identification in Biogeography by Ganapathy, G., Goodson, B., Jansen, R., Hai-son Le, Ramachandran, V., Warnow, T.

“…Identifying common patterns among area cladograms that arise in historical biogeography is an important tool for biogeographical inference. We develop the…”
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Statistical binning enables an accurate coalescent-based estimation of the avian tree by Mirarab, Siavash, Bayzid, Md. Shamsuzzoha, Boussau, Bastien, Warnow, Tandy

“…Gene tree incongruence arising from incomplete lineage sorting (ILS) can reduce the accuracy of concatenation-based estimations of species trees. Although…”
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Unidentifiable divergence times in rates-across-sites models by Evans, S.N., Warnow, T.

“…The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the…”
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Toward new software for computational phylogenetics by Moret, B.M.E., Li-San Wang, Warnow, T.

“…Systematists study how a group of genes or organisms evolved. These biologists now have set their sights on the Tree of Life challenge: to reconstruct the…”
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Disk-covering, a fast-converging method for phylogenetic tree reconstruction by Huson, D H, Nettles, S M, Warnow, T J

“…The evolutionary history of a set of species is represented by a phylogenetic tree, which is a rooted, leaf-labeled tree, where internal nodes represent…”
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A few logs suffice to build (almost) all trees: Part II by Erdös, Péter L., Steel, Michael A., Székely, LászlóA., Warnow, Tandy J.

“…Inferring evolutionary trees is an interesting and important problem in biology, but one that is computationally difficult as most associated optimization…”
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A robust model for finding optimal evolutionary trees by Farach, M., Kannan, S., Warnow, T.

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New approaches for reconstructing phylogenies from gene order data by Moret, Bernard M.E., Wang, Li-San, Warnow, Tandy, Wyman, Stacia K.

“…We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Our mathematical techniques include new polynomial-time methods…”
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The hardness of perfect phylogeny, feasible register assignment and other problems on thin colored graphs by Bodlaender, Hans L., Fellows, Michael R., Hallett, Michael T., Wareham, H.Todd, Warnow, Tandy J.

“…In this paper, we consider the complexity of a number of combinatorial problems; namely, Intervalizing Colored Graphs (DNA physical mapping), Triangulating…”
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Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree" by Mirarab, Siavash, Bayzid, Md Shamsuzzoha, Boussau, Bastien, Warnow, Tandy

“…Liu and Edwards argue against the use of weighted statistical binning within a species tree estimation pipeline. However, we show that their mathematical…”
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Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm by Snir, Sagi, Warnow, Tandy, Rao, Satish

“…Quartet-based phylogeny reconstruction methods, such as Quartet Puzzling, were introduced in the hope that they might be competitive with maximum likelihood…”
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Indo-European and Computational Cladistics by Ringe, Don, Warnow, Tandy, Taylor, Ann

“…This paper reports the results of an attempt to recover the first‐order subgrouping of the Indo‐European family using a new computational method devised by the…”
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The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation by Li-San Wang, Leebens-Mack, J, Wall, P Kerr, Beckmann, K, de Pamphilis, C W, Warnow, T

“…Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will…”
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Determining the Evolutionary Tree Using Experiments by Kannan, Sampath K., Lawler, Eugene L., Warnow, Tandy J.

“…Evolutionary trees, also known asphylogenetic trees, are rooted vertex-labeled trees which describe the evolution of a species setSfrom a common ancestor. The…”
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