Search Results - Phylogeny Computer algorithms. Algorithms.*

Fast tumor phylogeny regression via tree-structured dual dynamic programming by Schmidt, Henri, Qi, Yuanyuan, Raphael, Benjamin J, El-Kebir, Mohammed

“… problem remains a bottleneck in both method design and implementation due to the lack of fast, specialized algorithms…”
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TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing by Boumajdi, Nasma, Bendani, Houda, Belyamani, Lahcen, Ibrahimi, Azeddine

“…, and inaccuracies when handling highly divergent sequences, which leads to the development of alignment-free (AF) algorithms…”
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The Carbon Footprint of Bioinformatics by Grealey, Jason, Lannelongue, Loïc, Saw, Woei-Yuh, Marten, Jonathan, Méric, Guillaume, Ruiz-Carmona, Sergio, Inouye, Michael

“…s (in kilograms of CO2 equivalent units, kgCO2e) using the freely available Green Algorithms calculator (www.green…”
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HTPheno: An image analysis pipeline for high-throughput plant phenotyping by Hartmann, Anja, Czauderna, Tobias, Hoffmann, Roberto, Stein, Nils, Schreiber, Falk

“… During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms…”
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Improving the performance of Bayesian phylogenetic inference under relaxed clock models by Zhang, Rong, Drummond, Alexei

“… But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms…”
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DNACLUST: accurate and efficient clustering of phylogenetic marker genes by Ghodsi, Mohammadreza, Liu, Bo, Pop, Mihai

“…Background Clustering is a fundamental operation in the analysis of biological sequence data. New DNA sequencing technologies have dramatically increased the…”
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Inferring Speciation Times under an Episodic Molecular Clock by Rannala, Bruce, Yang, Ziheng, Anderson, Frank

“…We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages…”
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Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction by Allman, Elizabeth S, Rhodes, John A, Sullivant, Seth

“…Frequencies of k-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We…”
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LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks by Hu, Jialu, Reinert, Knut

“… Local network alignment is one of key systematic ways for predicting protein functions, identifying functional modules and understanding the phylogeny from these data…”
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Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation by McCormick, Elizabeth M., Lott, Marie T., Dulik, Matthew C., Shen, Lishuang, Attimonelli, Marcella, Vitale, Ornella, Karaa, Amel, Bai, Renkui, Pineda‐Alvarez, Daniel E., Singh, Larry N., Stanley, Christine M., Wong, Stacey, Bhardwaj, Anshu, Merkurjev, Daria, Mao, Rong, Sondheimer, Neal, Zhang, Shiping, Procaccio, Vincent, Wallace, Douglas C., Gai, Xiaowu, Falk, Marni J.

“…Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal…”
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A novel recombinant variant of latent membrane protein 1 from Epstein Barr virus in Argentina denotes phylogeographical association by Gantuz, Magdalena, Lorenzetti, Mario Alejandro, Chabay, Paola Andrea, Preciado, María Victoria

“…+ lymphomas were included. LMP1 was amplified by nested PCR and sequenced. Phylogenetic reconstructions were made under Maximun Likelihood, Bayesian and coalescent algorithms…”
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Exploring Current Challenges and Perspectives for Automatic Reconstruction of Clonal Evolution by Sandmann, Sarah, Richter, Silja, Jiang, Xiaoyi, Varghese, Julian

“…In the field of cancer research, reconstructing clonal evolution is of major interest. The technique provides new insights for analysis and prediction of tumor…”
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Interpretable metric learning in comparative metagenomics: The adaptive Haar-like distance by Gorman, Evan D., Lladser, Manuel E.

“…, split or bifurcation) of a reference phylogeny, indicating the relative importance of that node in discerning environmental samples based on their microbial…”
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Treelink: data integration, clustering and visualization of phylogenetic trees by Allende, Christian, Sohn, Erik, Little, Cedric

“…Background Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of…”
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Evolution and conservation genetics of an insular hemiparasitic plant lineage at the limit of survival: the case of Thesium sect. Kunkeliella in the Canary Islands by Rodríguez‐Rodríguez, Priscila, Fernández de Castro, Alejandro G., Pérez de Paz, Pedro Luis, Curbelo, Leticia, Palomares, Ángel, Mesa, Ricardo, Acevedo, Aurelio, Sosa, Pedro A.

“…Premise The diversification of island flora has been widely studied. However, the role of environmental niches in insular radiation processes has been less…”
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Bounds for phylogenetic network space metrics by Francis, Andrew, Huber, Katharina T., Moulton, Vincent, Wu, Taoyang

“…Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted…”
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Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification by Martin, Christian, Diaz, Naryttza N., Ontrup, Jörg, Nattkemper, Tim W.

“… To achieve reasonable binnings and classifications, DNA fragment structure has to be represented appropriately, so it can be processed by machine learning algorithms. Results…”
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EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences by Hu, Jianjun, Yang, Yifeng D, Kihara, Daisuke

“…s. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years…”
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Using tree diversity to compare phylogenetic heuristics by Sul, Seung-Jin, Matthews, Suzanne, Williams, Tiffani L

“… Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best…”
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Fast optimization of statistical potentials for structurally constrained phylogenetic models by Bonnard, Cécile, Kleinman, Claudia L, Rodrigue, Nicolas, Lartillot, Nicolas

“… However, the method required numerical estimations by the use of computationally heavy Markov Chain Monte Carlo sampling algorithms…”
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