Cargando…

Comparison of methods for estimating the nucleotide substitution matrix

BACKGROUND: The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matri...

Descripción completa

Detalles Bibliográficos
Autores principales:	Oscamou, Maribeth, McDonald, Daniel, Yap, Von Bing, Huttley, Gavin A, Lladser, Manuel E, Knight, Rob
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2008
Materias:	Research Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655096/ https://www.ncbi.nlm.nih.gov/pubmed/19046431 http://dx.doi.org/10.1186/1471-2105-9-511

Ejemplares similares

The Embedding Problem for Markov Models of Nucleotide Substitution
por: Verbyla, Klara L., et al.
Publicado: (2013)

Standard Codon Substitution Models Overestimate Purifying Selection for Nonstationary Data
por: Kaehler, Benjamin D., et al.
Publicado: (2017)

Pitfalls of the most commonly used models of context dependent substitution
por: Lindsay, Helen, et al.
Publicado: (2008)

Pitfalls of the most commonly used models of context dependent substitution
por: Lindsay, Helen, et al.
Publicado: (2009)

Genetic Distance for a General Non-Stationary Markov Substitution Process
por: Kaehler, Benjamin D., et al.
Publicado: (2015)

Estimates of the Effect of Natural Selection on Protein-Coding Content
por: Yap, Von Bing, et al.
Publicado: (2010)

Using the nucleotide substitution rate matrix to detect horizontal gene transfer
por: Hamady, Micah, et al.
Publicado: (2006)

Pathological rate matrices: from primates to pathogens
por: Schranz, Harold W, et al.
Publicado: (2008)

Species abundance information improves sequence taxonomy classification accuracy
por: Kaehler, Benjamin D., et al.
Publicado: (2019)

redbiom: a Rapid Sample Discovery and Feature Characterization System
por: McDonald, Daniel, et al.
Publicado: (2019)

Estimation of Distribution Overlap of Urn Models
por: Hampton, Jerrad, et al.
Publicado: (2012)

Correction: Estimation of Distribution Overlap of Urn Models
por: Hampton, Jerrad, et al.
Publicado: (2014)

Clusters of Nucleotide Substitutions and Insertion/Deletion Mutations Are Associated with Repeat Sequences
por: McDonald, Michael J., et al.
Publicado: (2011)

Rooting a phylogenetic tree with nonreversible substitution models
por: Yap, Von Bing, et al.
Publicado: (2005)

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
por: Caporaso, J Gregory, et al.
Publicado: (2008)

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals
por: Gaffney, Daniel J, et al.
Publicado: (2008)

The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates
por: Cloete, Leendert J, et al.
Publicado: (2014)

jmodeltest.org: selection of nucleotide substitution models on the cloud
por: Santorum, Jose Manuel, et al.
Publicado: (2014)

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search
por: Su, Xiaoquan, et al.
Publicado: (2020)

Visualization of nucleotide substitutions in the (micro)transcriptome
por: Naqvi, Ammar, et al.
Publicado: (2014)

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data
por: Armstrong, George, et al.
Publicado: (2022)

Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation
por: Janzen, Thijs, et al.
Publicado: (2021)

Statistical methods for detecting periodic fragments in DNA sequence data
por: Epps, Julien, et al.
Publicado: (2011)

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes
por: Miyazawa, Sanzo
Publicado: (2011)

Exploiting CpG Hypermutability to Identify Phenotypically Significant Variation Within Human Protein-Coding Genes
por: Ying, Hua, et al.
Publicado: (2011)

Regional Context in the Alignment of Biological Sequence Pairs
por: Sammut, Raymond, et al.
Publicado: (2010)

Quantifying Influences on Intragenomic Mutation Rate
por: Simon, Helmut, et al.
Publicado: (2020)

The Impact of Recombination on Nucleotide Substitutions in the Human Genome
por: Duret, Laurent, et al.
Publicado: (2008)

Hotspots of Biased Nucleotide Substitutions in Human Genes
por: Berglund, Jonas, et al.
Publicado: (2009)

Empirical codon substitution matrix
por: Schneider, Adrian, et al.
Publicado: (2005)

One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate
por: Hicks, Allison L, et al.
Publicado: (2012)

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
por: Amir, Amnon, et al.
Publicado: (2017)

A comparison of methods for estimating substitution rates from ancient DNA sequence data
por: Tong, K. Jun, et al.
Publicado: (2018)

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
por: Bokulich, Nicholas A., et al.
Publicado: (2018)

Genome-Wide Heterogeneity of Nucleotide Substitution Model Fit
por: Arbiza, Leonardo, et al.
Publicado: (2011)

Patterns of nucleotides that flank substitutions in human orthologous genes
por: Ma, Lei, et al.
Publicado: (2010)

Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments
por: Wu, Chieh-Hsi, et al.
Publicado: (2013)

Does the choice of nucleotide substitution models matter topologically?
por: Hoff, Michael, et al.
Publicado: (2016)

Accumulation of nucleotide substitutions occurring during experimental transmission of foot-and-mouth disease virus
por: Juleff, Nicholas, et al.
Publicado: (2013)

Assessing the Applicability of the GTR Nucleotide Substitution Model Through Simulations
por: Gatto, Laurent, et al.
Publicado: (2007)

Cannot write session to /tmp/vufind_sessions/sess_vg9ie3j7bisd2068d758fg4dtp