Cargando…

An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella

Comparative genomics based on whole genome sequencing (WGS) is increasingly being applied to investigate questions within evolutionary and molecular biology, as well as questions concerning public health (e.g., pathogen outbreaks). Given the impact that conclusions derived from such analyses may hav...

Descripción completa

Detalles Bibliográficos
Autores principales:	Pettengill, James B., Luo, Yan, Davis, Steven, Chen, Yi, Gonzalez-Escalona, Narjol, Ottesen, Andrea, Rand, Hugh, Allard, Marc W., Strain, Errol
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	PeerJ Inc. 2014
Materias:	Bioinformatics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201946/ https://www.ncbi.nlm.nih.gov/pubmed/25332847 http://dx.doi.org/10.7717/peerj.620

Ejemplares similares

TreeToReads - a pipeline for simulating raw reads from phylogenies
por: McTavish, Emily Jane, et al.
Publicado: (2017)

Phylogenetics and Differentiation of Salmonella Newport Lineages by Whole Genome Sequencing
por: Cao, Guojie, et al.
Publicado: (2013)

Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples
por: Pettengill, James B., et al.
Publicado: (2016)

Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere
por: Ottesen, Andrea R., et al.
Publicado: (2013)

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples
por: Kayikcioglu, Tunc, et al.
Publicado: (2023)

Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations
por: Pightling, Arthur W., et al.
Publicado: (2018)

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination
por: Pightling, Arthur W., et al.
Publicado: (2019)

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads
por: Commichaux, Seth, et al.
Publicado: (2021)

Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes
por: Chen, Yi, et al.
Publicado: (2016)

Whole genome phylogeny for 21 Drosophila species using predicted 2b-RAD fragments
por: Seetharam, Arun S., et al.
Publicado: (2013)

Whole-Genome Sequencing Analysis of Salmonella enterica Serovar Enteritidis Isolates in Chile Provides Insights into Possible Transmission between Gulls, Poultry, and Humans
por: Toro, Magaly, et al.
Publicado: (2016)

Identification of Salmonella for public health surveillance using whole genome sequencing
por: Ashton, Philip M., et al.
Publicado: (2016)

The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica
por: Pettengill, James B., et al.
Publicado: (2014)

Comparative Sequence Analysis of Multidrug-Resistant IncA/C Plasmids from Salmonella enterica
por: Hoffmann, Maria, et al.
Publicado: (2017)

VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs
por: Subramanian, Sankar, et al.
Publicado: (2019)

Draft Genome Sequences of 33 Salmonella enterica Clinical and Wildlife Isolates from Chile
por: Toro, Magaly, et al.
Publicado: (2015)

PRAWNS: compact pan-genomic features for whole-genome population genomics
por: Javkar, Kiran, et al.
Publicado: (2022)

Genome rearrangements and phylogeny reconstruction in Yersinia pestis
por: Bochkareva, Olga O., et al.
Publicado: (2018)

Molecular timetrees using relaxed clocks and uncertain phylogenies
por: Barba-Montoya, Jose, et al.
Publicado: (2023)

PTree: pattern-based, stochastic search for maximum parsimony phylogenies
por: Gregor, Ivan, et al.
Publicado: (2013)

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)
por: Ottesen, Andrea R, et al.
Publicado: (2013)

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

Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1
por: Li, Qingmei, et al.
Publicado: (2022)

Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition
por: Lee, Jover, et al.
Publicado: (2023)

Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017
por: González-Escalona, Narjol, et al.
Publicado: (2019)

Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters
por: Timme, Ruth E., et al.
Publicado: (2013)

On the Evolutionary History, Population Genetics and Diversity among Isolates of Salmonella Enteritidis PFGE Pattern JEGX01.0004
por: Allard, Marc W., et al.
Publicado: (2013)

CAM: an alignment-free method to recover phylogenies using codon aversion motifs
por: Miller, Justin B., et al.
Publicado: (2019)

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
por: Timme, Ruth E., et al.
Publicado: (2017)

BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU
por: Luo, Ruibang, et al.
Publicado: (2014)

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
por: Shapiro, Jason W., et al.
Publicado: (2021)

Closed Genome Sequence of Salmonella enterica Serovar Richmond Strain CFSAN000191, Obtained with Nanopore Sequencing
por: González-Escalona, Narjol, et al.
Publicado: (2018)

Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas
por: Yang, Lingpeng, et al.
Publicado: (2019)

Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana
por: Hudson, Lauren K., et al.
Publicado: (2020)

Time-calibrated phylogeny and full mitogenome sequence of the Galapagos sea lion (Zalophus wollebaeki) from scat DNA
por: Asadobay, Pacarina, et al.
Publicado: (2023)

Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis
por: den Bakker, Henk C., et al.
Publicado: (2014)

Middle Pleistocene protein sequences from the rhinoceros genus Stephanorhinus and the phylogeny of extant and extinct Middle/Late Pleistocene Rhinocerotidae
por: Welker, Frido, et al.
Publicado: (2017)

Comparison of commercial RNA extraction kits for preparation of DNA-free total RNA from Salmonella cells
por: Rump, Lydia V, et al.
Publicado: (2010)

Characterization of Vibrio parahaemolyticus clinical strains from Maryland (2012–2013) and comparisons to a locally and globally diverse V. parahaemolyticus strains by whole-genome sequence analysis
por: Haendiges, Julie, et al.
Publicado: (2015)

Whole genome sequencing of group A Streptococcus: development and evaluation of an automated pipeline for emmgene typing
por: Kapatai, Georgia, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_dpdg5iddgcfoppmthb1ac12nvh