An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella (Q30863381)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

whole genome sequencing

1 reference

3

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21 February 2020

Narjol Gonzalez-Escalona

5

1 reference

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21 February 2020

author name string

James B Pettengill

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Yan Luo

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Yi Chen

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Andrea Ottesen

6

1 reference

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21 February 2020

Hugh Rand

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Marc W Allard

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

Errol Strain

9

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21 February 2020

publication date

14 October 2014

1 reference

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21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

volume

2

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21 February 2020

page(s)

e620

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

21 February 2020

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

A composite genome approach to identify phylogenetically informative data from next-generation sequencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Automated reconstruction of whole-genome phylogenies from short-sequence reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Benchmarking short sequence mapping tools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

GAGE-B: an evaluation of genome assemblers for bacterial organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Next-generation sequencing platforms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Performance comparison of benchtop high-throughput sequencing platforms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Fast gapped-read alignment with Bowtie 2

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

GAGE: A critical evaluation of genome assemblies and assembly algorithms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Bacterial epidemiology and biology - lessons from genome sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Comparative analysis of algorithms for next-generation sequencing read alignment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

phangorn: phylogenetic analysis in R

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

The origin of the Haitian cholera outbreak strain

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

FastTree 2--approximately maximum-likelihood trees for large alignments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Evaluation of next generation sequencing platforms for population targeted sequencing studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Next-generation DNA sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Versatile and open software for comparing large genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

APE: Analyses of Phylogenetics and Evolution in R language

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

A likelihood approach to estimating phylogeny from discrete morphological character data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4201946

Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals.

21 June 2018

1 reference

A genealogical approach to quantifying lineage divergence.

21 January 2018

1 reference

Updating benchtop sequencing performance comparison

21 January 2018

1 reference

Reply to "South Asia instead of Nepal may be the origin of the Haitian cholera outbreak strain".

21 January 2018

1 reference

Identification of a salmonellosis outbreak by means of molecular sequencing.

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.7717/PEERJ.620

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json

21 February 2020

PubMed publication ID

25332847

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25332847%20AND%20SRC:MED&resulttype=core&format=json