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snpTree specifications


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


  • person_outline Pimlapas Leekitcharoenphon

Publication for snpTree

snpTree citations


Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

Front Microbiol
PMCID: 5744012
PMID: 29312260
DOI: 10.3389/fmicb.2017.02587

[…] logenetic 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 proporti […]


In Vitro Tolerance of Drug Naive Staphylococcus aureus Strain FDA209P to Vancomycin

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

[…] er 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 single-nu […]


Bacterial whole genome based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods

BMC Genomics
PMCID: 5217230
PMID: 28056767
DOI: 10.1186/s12864-016-3407-6

[…] etermining epidemiological relationships [, ], and a number of methods for inferring phylogenies directly from NGS data have been created. Methods available online which accept raw reads data include snpTree [], NDtree [, ] and CSI Phylogeny [] available from Center for Genomic Epidemiology. Furthermore REALPHY from the Swiss Institute of Bioinformatics is also online available and can be download […]


Genome Sequence of Airborne Acinetobacter sp. Strain 5 2Ac02 in the Hospital Environment, Close to the Species of Acinetobacter towneri

Genome Announc
PMCID: 5146438
PMID: 27932646
DOI: 10.1128/genomeA.01343-16
call_split See protocol

[…] ds (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 Dalto […]


Rapid Acquisition of Linezolid Resistance in Methicillin Resistant Staphylococcus aureus: Role of Hypermutation and Homologous Recombination

PLoS One
PMCID: 4868352
PMID: 27182700
DOI: 10.1371/journal.pone.0155512
call_split See protocol

[…] open reading frames (ORFs) and annotated using RAST [] and BLAST [].The resulting M2 chromosome scaffold was compared to the published ST5 S. aureus reference complete genomes (N315, Mu3, Mu50) using snpTree-1.1 [] to construct a SNP phylogenetic tree. We compared the M2 and N315 genomes for homologs using BlastP bidirectional best hit analysis with an identity threshold of 60% and an E-value thre […]


Parallel Evolution in Streptococcus pneumoniae Biofilms

Genome Biol Evol
PMCID: 4898793
PMID: 27190203
DOI: 10.1093/gbe/evw072

[…] , their 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 were […]


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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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