nextstrain statistics

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Protocols

nextstrain specifications

Information


Unique identifier OMICS_16595
Name nextstrain
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Viruses
    • Ebola virus
    • Influenza A virus
    • Influenza A virus (A/Puerto Rico/8/1934(H1N1))
    • Influenza B virus

Subtools


  • janus
  • phyloTree
  • react-sidebar
  • react-svg-pan-zoom

Maintainers


  • person_outline Trevor Bedford
  • person_outline James Hadfield
  • person_outline Richard Neher
  • person_outline Trevor Bedford

Additional information


https://github.com/nextstrain

Publication for nextstrain

nextstrain citations

 (194)
library_books

The MT CO1 V83I Polymorphism is a Risk Factor for Primary Open Angle Glaucoma in African American Men

2018
PMCID: 5886029
PMID: 29610859
DOI: 10.1167/iovs.17-23277

[…] Build 17 of PhyloTree (available in the public domain at www.phylotree.org) and the MITOMAP and MITOMASTER databases (available in the public domain at www.mitomap.org) were used to associate the observed mtDNA v […]

library_books

Maternal DNA lineages at the gate of Europe in the 10th century AD

2018
PLoS One
PMCID: 5851556
PMID: 29538439
DOI: 10.1371/journal.pone.0193578

[…] g region polymorphic positions were inferred by comparison to the revised Cambridge Reference Sequence (rCRS: NC_012920.1) []. Haplogroups were assigned using the HaploGrep2 web application, based on PhyloTree built 17 [, ]. […]

library_books

Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

2018
Proc Natl Acad Sci U S A
PMCID: 5879675
PMID: 29531053
DOI: 10.1073/pnas.1717762115

[…] the most likely haplogroup for mitochondrial consensus sequences. Y chromosomal haplogroups were assigned by investigating up to 732 haplotype-informative single base substitutions obtained from the Phylotree version of March 9, 2016 (). Sites presenting more than one allele were not taken into account for the classification. Derived sites for all samples are shown in Dataset S1. See SI Appendix, […]

call_split

Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

2018
PLoS One
PMCID: 5844571
PMID: 29522562
DOI: 10.1371/journal.pone.0194223
call_split See protocol

[…] avoid alignment errors. SNPs were identified and haplogroups were assigned using Haplogrep 2.0 (http://haplogrep.uibk.ac.at/) [] with the assistance of Mitomap (http://www.mitomap.org/MITOMAP) [] and PhyloTree (http://www.Phylotree.org) []. […]

library_books

Biological Sexing of a 4000 Year Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

2018
Genes
PMCID: 5867856
PMID: 29494531
DOI: 10.3390/genes9030135

[…] ntamMix [] and by evaluating the number of human sequences observed in the extraction (RB) and library preparation control (NC) samples. The mtDNA haplogroup of the final profile was determined using Phylotree build 17 [] and HaploGrep 2.0 []. Finally, the sequence was compared to other mtDNA sequences from modern and ancient populations stored in GenBank, the European Nucleotide Archives database […]

library_books

Deep Coverage MPS Analysis of Heteroplasmic Variants within the mtGenome Allows for Frequent Differentiation of Maternal Relatives

2018
Genes
PMCID: 5867845
PMID: 29495418
DOI: 10.3390/genes9030124

[…] Haplogroups were established using the collated major haplotype data and the Mitotool algorithm [] incorporating Phylotree build 15 or 16 []. […]

Citations

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nextstrain institution(s)
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA; Max Planck Institute for Developmental Biology, Tübingen, Germany; Biozentrum, University of Basel, Basel, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
nextstrain funding source(s)
Supported by the Open Science Prize, by the NSF through DGE-1256082, by the ERC through StG-260686 and by NIH R35 GM119774-01.

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