Cargando…

Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty

BACKGROUND: Multiple sequence alignments (MSAs) represent the fundamental unit of data inputted to most comparative sequence analyses. In phylogenetic analyses in particular, errors in MSA construction have the potential to induce further errors in downstream analyses such as phylogenetic reconstruc...

Descripción completa

Detalles Bibliográficos
Autores principales:	Spielman, Stephanie J., Miraglia, Molly L.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2021
Materias:	Research
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8628390/ https://www.ncbi.nlm.nih.gov/pubmed/34844571 http://dx.doi.org/10.1186/s12862-021-01931-5

Ejemplares similares

Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model
por: Spielman, Stephanie J, et al.
Publicado: (2018)

The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life
por: Du, Yan, et al.
Publicado: (2019)

Parameterizing sequence alignment with an explicit evolutionary model
por: Rivas, Elena, et al.
Publicado: (2015)

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
por: Jayaraman, Gayathri, et al.
Publicado: (2010)

Multiple sequence alignment accuracy and evolutionary distance estimation
por: Rosenberg, Michael S
Publicado: (2005)

Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix
por: Ndhlovu, Andrew, et al.
Publicado: (2015)

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
por: Herman, Joseph L, et al.
Publicado: (2015)

Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty
por: Md Mukarram Hossain, A.S., et al.
Publicado: (2015)

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment
por: Altschul, Stephen F., et al.
Publicado: (2010)

Fast and sensitive multiple alignment of large genomic sequences
por: Brudno, Michael, et al.
Publicado: (2003)

A model of evolution and structure for multiple sequence alignment
por: Löytynoja, Ari, et al.
Publicado: (2008)

Modeling Diagnostic Expertise in Cases of Irreducible Uncertainty: The Decision-Aligned Response Model
por: Pusic, Martin V., et al.
Publicado: (2022)

Advantages of a Mechanistic Codon Substitution Model for Evolutionary Analysis of Protein-Coding Sequences
por: Miyazawa, Sanzo
Publicado: (2011)

Antibody-Specific Model of Amino Acid Substitution for Immunological Inferences from Alignments of Antibody Sequences
por: Mirsky, Alexander, et al.
Publicado: (2015)

Relative evolutionary rate inference in HyPhy with LEISR
por: Spielman, Stephanie J., et al.
Publicado: (2018)

Accurate statistical model of comparison between multiple sequence alignments
por: Sadreyev, Ruslan I., et al.
Publicado: (2008)

Modeling variation of clinical team processes with multiple sequence alignment
por: Bahr, Nathan J, et al.
Publicado: (2019)

Leveraging protein language models for accurate multiple sequence alignments
por: McWhite, Claire D., et al.
Publicado: (2023)

Consequences of Substitution Model Selection on Protein Ancestral Sequence Reconstruction
por: Del Amparo, Roberto, et al.
Publicado: (2022)

Accounting For Alignment Uncertainty in Phylogenomics
por: Wu, Martin, et al.
Publicado: (2012)

Multiple Sequence Alignment
Publicado: (2008)

MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments
por: Collingridge, Peter W, et al.
Publicado: (2012)

The Cumulative Indel Model: Fast and Accurate Statistical Evolutionary Alignment
por: De Maio, Nicola
Publicado: (2020)

SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment
por: Barlowe, Scott, et al.
Publicado: (2017)

Optimizing substitution matrix choice and gap parameters for sequence alignment
por: Edgar, Robert C
Publicado: (2009)

Substitution matrix based color schemes for sequence alignment visualization
por: Kunzmann, Patrick, et al.
Publicado: (2020)

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments
por: Minami, Shintaro, et al.
Publicado: (2013)

Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
por: Seemann, Stefan E., et al.
Publicado: (2008)

Application of probabilistic modelling for the uncertainty evaluation of alignment measurements of large accelerator magnets assemblies
por: Doytchinov, Iordan Petrov, et al.
Publicado: (2018)

Modelling survival: exposure pattern, species sensitivity and uncertainty
por: Ashauer, Roman, et al.
Publicado: (2016)

Contextual Multiple Sequence Alignment
por: Gambin, Anna, et al.
Publicado: (2005)

Evolutionary distance estimation and fidelity of pair wise sequence alignment
por: Rosenberg, Michael S
Publicado: (2005)

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments
por: Garrigan, Daniel
Publicado: (2013)

Graph-based modeling of tandem repeats improves global multiple sequence alignment
por: Szalkowski, Adam M., et al.
Publicado: (2013)

Protein language models trained on multiple sequence alignments learn phylogenetic relationships
por: Lupo, Umberto, et al.
Publicado: (2022)

Generative power of a protein language model trained on multiple sequence alignments
por: Sgarbossa, Damiano, et al.
Publicado: (2023)

Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors
por: Spielman, Stephanie J., et al.
Publicado: (2015)

Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics
por: Spielman, Stephanie J
Publicado: (2020)

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
por: Sela, Itamar, et al.
Publicado: (2015)

Improved mitochondrial amino acid substitution models for metazoan evolutionary studies
por: Le, Vinh Sy, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_r6maqbaf2vh7pko8fr87m30cis