snpTree statistics

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Citations per year

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Popular tool citations

chevron_left Phylogenetic network construction SNP detection chevron_right
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Associated diseases

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Protocols

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snpTree specifications

Information


Unique identifier OMICS_21963
Name snpTree
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pimlapas Leekitcharoenphon <>

Publication for snpTree

snpTree in pipeline

2014
PMCID: 4041001
PMID: 24803570
DOI: 10.1093/gbe/evu094

[…] that e. anophelis and e. meningoseptica genomes belong to distinct groups (). single-nucleotide polymorphism (snp) differences between each pair of elizabethkingia spp. was calculated using the snptree web server () and shown in . these results showed that the genomes of the patient isolates from the current outbreak (nuhp1, nuhp2, and nuhp3) were very similar to each other, nuh1 and nuh4, […]


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snpTree in publications

 (15)
PMCID: 5744012
PMID: 29312260
DOI: 10.3389/fmicb.2017.02587

[…] tree from assembled genomes or sets of sequence reads just by a mere upload of data. among the tools which accept raw sequence reads and performs basics bioinformatics analysis also include snptree (leekitcharoenphon et al., ), nucleotide difference tree (ndtree) (leekitcharoenphon et al., ) and csi phylogeny (kaas et al., ). interestingly, these techniques exclude a significant […]

PMCID: 5278750
PMID: 27855063
DOI: 10.1128/AAC.01154-16

[…] to detect genetic alterations in the survivor strains, the 250-bp paired-end sequencing reads were mapped to the complete reference genome sequence of parental strain fda209p () using the programs snptree (v1.1) and csi phylogeny (v1.1) (). the average percentage of the reference genome mapped was 99.94%, indicating that the number of reads in this analysis was sufficient., the detected […]

PMCID: 5146438
PMID: 27932646
DOI: 10.1128/genomeA.01343-16

[…] (2014), and disinfectant susceptibility testing was performed by microdilution. phylogenetic analysis was carried out by average nucleotide identity (ani), single nucleotide polymorphism analysis (snptree), and rna polymerase beta subunit sequence (rpob) analysis. a matrix-assisted laser desorption ionization–time of flight mass spectrometry (maldi-tof ms) dendrogram was generated (bruker […]

PMCID: 4898793
PMID: 27190203
DOI: 10.1093/gbe/evw072

[…] position, and quality metrics. variants were filtered based on quality score (q value) and those with q values <20 were rejected. alternatively, variant call files (.vcf) were generated using snptree1.1 (). each mutation was manually curated by mapping the illumina fastq files against the wt reference to generate bam files (.bam) and indexed bam files (.bai) using samtools. bam files […]

PMCID: 4828450
PMID: 27148176
DOI: 10.3389/fmicb.2016.00478

[…] scotland and public health england., the serum staten institute in copenhagen, denmark sequenced 42 isolates received in a 7-week period and determined their relationship using their web-based tools snptree and ndtree (joensen et al., ). during this study period they had an outbreak with 13 cases of e. coli o157:h7, six of which were included in their study. the ndtree method, an assembly-free […]


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snpTree institution(s)
National Food Institute, Technical University of Denmark, Lyngby, Denmark; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Denmark
snpTree funding source(s)
Supported by the Center for Genomic Epidemiology (09- 067103/DSF), Danish Food Industry Agency (3304-FVFP-08) and the Technical University of Denmark.

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