Phylogenetic Assignment of Named Global Outbreak Lineages (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Phylogenetic Assignment of Named Global Outbreak Lineages" in English language version.

refsWebsite

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8nih.gov

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7web.archive.org

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5doi.org

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3github.com

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2cnn.com

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1pathogensurveillance.net

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1semanticscholar.org

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1virological.org

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1oup.com

485^th place

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1worldcat.org

5^th place

1network.org

low place

1scikit-learn.org

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1pango.network

low place

1cog-uk.io

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1who.int

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1whn.global

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1time.com

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1wsj.com

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1standard.co.uk

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1theweek.com

2,909^th place

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cnn.com (Global: 28^th place; English: 26^th place)

cnn.com

Jen Christensen (20 December 2023). "XBB.1.5, BA.2.86, JN.1: How to understand the Covid-19 alphabet soup". CNN. Retrieved 26 November 2025.

edition.cnn.com

Brenda Goodman (13 January 2023). "Why no Pi? Variants are still stuck on Omicron even as coronavirus continues to mutate". CNN. Retrieved 26 November 2025.

cog-uk.io (Global: low place; English: low place)

pangolin.cog-uk.io

"Pangolin COVID-19 Lineage Assigner". pangolin.cog-uk.io. Archived from the original on 10 February 2021. Retrieved 13 February 2021.

doi.org (Global: 2^nd place; English: 2^nd place)

O'Toole, Áine; Scher, Emily; Underwood, Anthony; Jackson, Ben; Hill, Verity; McCrone, John T; Colquhoun, Rachel; Ruis, Chris; Abu-Dahab, Khalil; Taylor, Ben; Yeats, Corin; Du Plessis, Louis; Maloney, Daniel; Medd, Nathan; Attwood, Stephen W; Aanensen, David M; Holmes, Edward C; Pybus, Oliver G; Rambaut, Andrew (5 July 2021). "Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool". Virus Evolution. 7 (2) veab064. doi:10.1093/ve/veab064. PMC 8344591. PMID 34527285.
Rambaut, A.; Holmes, E.C.; O'Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096.
Rambaut, Andrew; Holmes, Edward C.; o'Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; Du Plessis, Louis; Pybus, Oliver G. (15 July 2020). "Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 6 (3): 415. doi:10.1038/s41564-021-00872-5. PMC 7845574. PMID 33514928.
Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. 38 (4). Oxford University Press (OUP): 1537–1543. doi:10.1093/molbev/msaa316. ISSN 0737-4038. PMC 7798932. PMID 33295605. Archived from the original on 10 December 2020. Retrieved 22 January 2021.
Jacob, Jobin John; Vasudevan, Karthick; Pragasam, Agila Kumari; Gunasekaran, Karthik; Kang, Gagandeep; Veeraraghavan, Balaji; Mutreja, Ankur (22 December 2020). "Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations". bioRxiv 10.1101/2020.12.22.423920. Phylogenetic Assignment of Named Global Outbreak LINeages tool (PANGOLIN) has been the most widely used tool for lineage assignment to newly emerging variants.

github.com (Global: 383^rd place; English: 320^th place)

"Release 4.3.4". 14 November 2025. Retrieved 16 November 2025.
"pangoLEARN Store of the trained model for PANGOLIN to access". GitHub: cov-lineages/pangoLEARN. Archived from the original on 3 January 2021. Retrieved 13 February 2021.
"cov-lineages/pangolin". GitHub: cov-lineages/pangolin. Archived from the original on 15 February 2021. Retrieved 13 February 2021.

network.org (Global: low place; English: low place)

pango.network.org

"PANGO lineages". pango.network. Retrieved 4 March 2021.

nih.gov (Global: 4^th place; English: 4^th place)

ncbi.nlm.nih.gov

O'Toole, Áine; Scher, Emily; Underwood, Anthony; Jackson, Ben; Hill, Verity; McCrone, John T; Colquhoun, Rachel; Ruis, Chris; Abu-Dahab, Khalil; Taylor, Ben; Yeats, Corin; Du Plessis, Louis; Maloney, Daniel; Medd, Nathan; Attwood, Stephen W; Aanensen, David M; Holmes, Edward C; Pybus, Oliver G; Rambaut, Andrew (5 July 2021). "Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool". Virus Evolution. 7 (2) veab064. doi:10.1093/ve/veab064. PMC 8344591. PMID 34527285.
Rambaut, A.; Holmes, E.C.; O'Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096.
Rambaut, Andrew; Holmes, Edward C.; o'Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; Du Plessis, Louis; Pybus, Oliver G. (15 July 2020). "Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 6 (3): 415. doi:10.1038/s41564-021-00872-5. PMC 7845574. PMID 33514928.
Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. 38 (4). Oxford University Press (OUP): 1537–1543. doi:10.1093/molbev/msaa316. ISSN 0737-4038. PMC 7798932. PMID 33295605. Archived from the original on 10 December 2020. Retrieved 22 January 2021.

pubmed.ncbi.nlm.nih.gov

O'Toole, Áine; Scher, Emily; Underwood, Anthony; Jackson, Ben; Hill, Verity; McCrone, John T; Colquhoun, Rachel; Ruis, Chris; Abu-Dahab, Khalil; Taylor, Ben; Yeats, Corin; Du Plessis, Louis; Maloney, Daniel; Medd, Nathan; Attwood, Stephen W; Aanensen, David M; Holmes, Edward C; Pybus, Oliver G; Rambaut, Andrew (5 July 2021). "Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool". Virus Evolution. 7 (2) veab064. doi:10.1093/ve/veab064. PMC 8344591. PMID 34527285.
Rambaut, A.; Holmes, E.C.; O'Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096.
Rambaut, Andrew; Holmes, Edward C.; o'Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; Du Plessis, Louis; Pybus, Oliver G. (15 July 2020). "Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 6 (3): 415. doi:10.1038/s41564-021-00872-5. PMC 7845574. PMID 33514928.
Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. 38 (4). Oxford University Press (OUP): 1537–1543. doi:10.1093/molbev/msaa316. ISSN 0737-4038. PMC 7798932. PMID 33295605. Archived from the original on 10 December 2020. Retrieved 22 January 2021.

oup.com (Global: 485^th place; English: 440^th place)

academic.oup.com

Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. 38 (4). Oxford University Press (OUP): 1537–1543. doi:10.1093/molbev/msaa316. ISSN 0737-4038. PMC 7798932. PMID 33295605. Archived from the original on 10 December 2020. Retrieved 22 January 2021.

pango.network (Global: low place; English: low place)

"pangoLEARN PANGOLIN 2.0: pangoLEARN description". pango.network. Retrieved 19 November 2021. The model was trained using ~60,000 SARS-CoV-2 sequences from GISAID... training this model takes approximately 30 minutes on our hardware

pathogensurveillance.net (Global: low place; English: low place)

"Real-Time Epidemiology for COVID-19". www.pathogensurveillance.net. Archived from the original on 17 January 2021. Retrieved 22 January 2021.

scikit-learn.org (Global: low place; English: low place)

"sklearn.tree.DecisionTreeClassifier". scikit-learn.org. Archived from the original on 19 February 2021. Retrieved 13 February 2021.

semanticscholar.org (Global: 11^th place; English: 8^th place)

api.semanticscholar.org

Rambaut, A.; Holmes, E.C.; O'Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096.

standard.co.uk (Global: 238^th place; English: 159^th place)

Hassan, Beril Naz; Hewitt, Sian (7 September 2023). "What is Pirola? Updated vaccine to counter Covid variant detected in UK and globally". Evening Standard. Retrieved 11 September 2023.

theweek.com (Global: 2,909^th place; English: 1,809^th place)

Arion McNicoll (12 January 2024). "Covid-19: what to know about UK's new Juno and Pirola variants". The Week. Retrieved 22 November 2025.

time.com (Global: 61^st place; English: 54^th place)

Jamie Ducharme (7 November 2022). "BQ.1, BQ.1.1, BF.7, and XBB: Why New COVID-19 Variants Have Such Confusing Names". Time. Retrieved 26 November 2025.

virological.org (Global: low place; English: low place)

"Pangolin web application release". virological.org. May 2020. Archived from the original on 10 February 2021. Retrieved 18 February 2021.

web.archive.org (Global: 1^st place; English: 1^st place)

"Real-Time Epidemiology for COVID-19". www.pathogensurveillance.net. Archived from the original on 17 January 2021. Retrieved 22 January 2021.
"Pangolin web application release". virological.org. May 2020. Archived from the original on 10 February 2021. Retrieved 18 February 2021.
Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. 38 (4). Oxford University Press (OUP): 1537–1543. doi:10.1093/molbev/msaa316. ISSN 0737-4038. PMC 7798932. PMID 33295605. Archived from the original on 10 December 2020. Retrieved 22 January 2021.
"pangoLEARN Store of the trained model for PANGOLIN to access". GitHub: cov-lineages/pangoLEARN. Archived from the original on 3 January 2021. Retrieved 13 February 2021.
"sklearn.tree.DecisionTreeClassifier". scikit-learn.org. Archived from the original on 19 February 2021. Retrieved 13 February 2021.
"cov-lineages/pangolin". GitHub: cov-lineages/pangolin. Archived from the original on 15 February 2021. Retrieved 13 February 2021.
"Pangolin COVID-19 Lineage Assigner". pangolin.cog-uk.io. Archived from the original on 10 February 2021. Retrieved 13 February 2021.

whn.global (Global: low place; English: low place)

T. Ryan Gregory; Yaneer Bar-Yam; Ulrich Elling; Daniele Focosi; Federico Gueli; Ryan Hisner; Mike Honey; Stuart Turville (13 February 2023). ""Common Names" for Notable SARS-CoV-2 Variants: Proposal for a Transparent and Consistent Nicknaming Process to Aid Communication". World Health Network. Retrieved 26 November 2025.

who.int (Global: 195^th place; English: 302^nd place)

"Statement on the update of WHO's working definitions and tracking system for SARS-CoV-2 variants of concern and variants of interest". World Health Organization. 16 March 2023. Retrieved 26 November 2025.

worldcat.org (Global: 5^th place; English: 5^th place)

search.worldcat.org

Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.). "Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny". Molecular Biology and Evolution. 38 (4). Oxford University Press (OUP): 1537–1543. doi:10.1093/molbev/msaa316. ISSN 0737-4038. PMC 7798932. PMID 33295605. Archived from the original on 10 December 2020. Retrieved 22 January 2021.

wsj.com (Global: 79^th place; English: 65^th place)

Brianna Abbott (18 September 2023). "He's Been Naming Covid Variants. Not Everyone's Happy". The Wall Street Journal. Retrieved 26 November 2025.

Phylogenetic Assignment of Named Global Outbreak Lineages (English Wikipedia)

cnn.com (Global: 28th place; English: 26th place)

cnn.com

edition.cnn.com

cog-uk.io (Global: low place; English: low place)

pangolin.cog-uk.io

doi.org (Global: 2nd place; English: 2nd place)

github.com (Global: 383rd place; English: 320th place)

network.org (Global: low place; English: low place)

pango.network.org

nih.gov (Global: 4th place; English: 4th place)

ncbi.nlm.nih.gov

pubmed.ncbi.nlm.nih.gov

oup.com (Global: 485th place; English: 440th place)

academic.oup.com

pango.network (Global: low place; English: low place)

pathogensurveillance.net (Global: low place; English: low place)

scikit-learn.org (Global: low place; English: low place)

semanticscholar.org (Global: 11th place; English: 8th place)

api.semanticscholar.org

standard.co.uk (Global: 238th place; English: 159th place)

theweek.com (Global: 2,909th place; English: 1,809th place)

time.com (Global: 61st place; English: 54th place)

virological.org (Global: low place; English: low place)

web.archive.org (Global: 1st place; English: 1st place)

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who.int (Global: 195th place; English: 302nd place)

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wsj.com (Global: 79th place; English: 65th place)

cnn.com (Global: 28^th place; English: 26^th place)

doi.org (Global: 2^nd place; English: 2^nd place)

github.com (Global: 383^rd place; English: 320^th place)

nih.gov (Global: 4^th place; English: 4^th place)

oup.com (Global: 485^th place; English: 440^th place)

semanticscholar.org (Global: 11^th place; English: 8^th place)

standard.co.uk (Global: 238^th place; English: 159^th place)

theweek.com (Global: 2,909^th place; English: 1,809^th place)

time.com (Global: 61^st place; English: 54^th place)

web.archive.org (Global: 1^st place; English: 1^st place)

who.int (Global: 195^th place; English: 302^nd place)

worldcat.org (Global: 5^th place; English: 5^th place)

wsj.com (Global: 79^th place; English: 65^th place)