201:. A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage (Pango lineage). Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage. Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage. This latter feature draws on publicly available genomes obtained from the
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et al. (2020), a Pango lineage is described as a cluster of sequences that are associated with an epidemiological event, for instance an introduction of the virus into a distinct geographic area with evidence of onward spread. Lineages are designed to capture the emerging edge of the pandemic and are
283:
Originally, PANGOLIN used a maximum-likelihood-based assignment algorithm to assign query SARS-CoV-2 the most likely lineage sequence. Since the release of
Version 2.0 in July 2020, however, it has used the 'pangoLEARN' machine-learning-based assignment algorithm to assign lineages to new SARS-CoV-2
309:
PANGOLIN was created by Áine O'Toole and the
Rambaut lab and released on 5 April 2020. The main developers of PANGOLIN are Áine O'Toole and Emily Scher; many others have contributed to various aspects of the tool, including Ben Jackson, J.T. McCrone, Verity Hill, and Rachel Colquhoun of the Rambaut
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is constructed from an alignment containing publicly available SARS-CoV-2 genomes, and sub-clusters of sequences in this tree are manually examined and cross-referenced against epidemiological information to designate new lineages; these can be designated by data producers, and lineage suggestions
379:
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;
270:
These manually curated lineage designations, and the associated genome sequences, are the input into the machine learning model training. This model, both the training and the assignment, has been termed 'pangoLEARN'. The current version of pangoLEARN uses a classification tree, based on the
688:
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".
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and from a GitHub repository, and as a web-application with a drag-and-drop graphical user interface. The PANGOLIN web application has assigned more than 512,000 unique SARS-CoV-2 sequences as of
January 2021.
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The PANGOLIN web application was developed by the Centre for
Genomic Pathogen Surveillance, namely Anthony Underwood, Ben Taylor, Corin Yeats, Khali Abu-Dahab, and David Aanensen.
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Phylogenetic
Assignment of Named Global Outbreak LINeages tool (PANGOLIN) has been the most widely used tool for lineage assignment to newly emerging variants.
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Rambaut, Andrew; Holmes, Edward C.; o'Toole, Áine; Hill, Verity; McCrone, John T.; Ruis, Christopher; Du
Plessis, Louis; Pybus, Oliver G. (15 July 2020).
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Distinct from the PANGOLIN tool, Pango lineages are regularly, manually curated based on the current globally circulating diversity. A large
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The model was trained using ~60,000 SARS-CoV-2 sequences from GISAID... training this model takes approximately 30 minutes on our hardware
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genomes. This approach is fast and can assign large numbers of SARS-CoV-2 genomes in a relatively short time.
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Pipes, Lenore; Wang, Hongru; Huelsenbeck, John P; Nielsen, Rasmus (9 December 2020). Malik, Harmit (ed.).
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International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
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189:. Its purpose is to implement a dynamic nomenclature (known as the Pango nomenclature) to classify
568:"Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology"
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Both the tool and the PANGOLIN nomenclature system have been used extensively during the
466:"A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology"
382:"Assignment of Epidemiological Lineages in an Emerging Pandemic Using the Pangolin Tool"
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Microsoft
Research - University of Trento Centre for Computational and Systems Biology
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PANGOLIN is a key component underpinning the Pango nomenclature system.
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177:) is a software tool developed by Dr. Áine O'Toole and members of the
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619:"Assessing Uncertainty in the Rooting of the SARS-CoV-2 Phylogeny"
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laboratory, with an associated web application developed by the
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714:"pangoLEARN Store of the trained model for PANGOLIN to access"
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African
Society for Bioinformatics and Computational Biology
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Rambaut, A.; Holmes, E.C.; O'Toole, Á.; et al. (2020).
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Max Planck Institute of Molecular Cell Biology and Genetics
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Phylogenetic Assignment of Named Global Outbreak Lineages
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Phylogenetic Assignment of Named Global Outbreak Lineages
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International Nucleotide Sequence Database Collaboration
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1001:, database of protein sequences grouping together
837:"pangoLEARN PANGOLIN 2.0: pangoLEARN description"
1236:US National Center for Biotechnology Information
1321:International Society for Computational Biology
629:(4). Oxford University Press (OUP): 1537–1543.
229:at a fine-grain resolution suitable to genomic
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275:implementation of a decision tree classifier.
1335:Institute of Genomics and Integrative Biology
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1364:European Conference on Computational Biology
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1580:Medical responses to the COVID-19 pandemic
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258:can be submitted to the Pango team via a
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1315:International Society for Biocuration
1213:European Molecular Biology Laboratory
883:from the original on 10 February 2021
817:from the original on 15 February 2021
784:from the original on 19 February 2021
774:"sklearn.tree.DecisionTreeClassifier"
754:from the original on 28 February 2021
669:from the original on 10 December 2020
547:from the original on 10 February 2021
430:"Real-Time Epidemiology for COVID-19"
323:Colloquial names of COVID-19 variants
7:
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873:"Pangolin COVID-19 Lineage Assigner"
847:from the original on 4 November 2021
440:from the original on 17 January 2021
1341:Japanese Society for Bioinformatics
724:from the original on 3 January 2021
1303:European Molecular Biology network
537:"Pangolin web application release"
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1393:Pacific Symposium on Biocomputing
1297:Australia Bioinformatics Resource
1264:Swiss Institute of Bioinformatics
1247:Netherlands Bioinformatics Centre
1207:European Bioinformatics Institute
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1195:Database Center for Life Science
1183:Computational Biology Department
1071:Arabidopsis Information Resource
1041:Specialised genomic databases:
718:GitHub: cov-lineages/pangoLEARN
623:Molecular Biology and Evolution
380:Rambaut, Andrew (5 July 2021).
296:-based tool, downloadable from
203:COVID-19 Genomics UK Consortium
138:GNU General Public License v3.0
27:SARS-CoV-2 lineage nomenclature
1242:Japanese Institute of Genetics
1:
1162:Rosalind (education platform)
1079:Zebrafish Information Network
1047:Saccharomyces Genome Database
811:GitHub: cov-lineages/pangolin
1492:List of biological databases
1011:Protein Information Resource
434:www.pathogensurveillance.net
233:and outbreak investigation.
231:epidemiological surveillance
205:and from those submitted to
985:European Nucleotide Archive
292:PANGOLIN is available as a
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585:10.1038/s41564-021-00872-5
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1270:Wellcome Sanger Institute
1224:J. Craig Venter Institute
696:10.1101/2020.12.22.423920
485:10.1038/s41564-020-0770-5
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1253:Philippine Genome Center
209:. It is named after the
197:, the virus that causes
1497:Molecular phylogenetics
993:China National GeneBank
807:"cov-lineages/pangolin"
305:Creators and developers
84:; 14 months ago
1565:Phylogenetics software
1201:DNA Data Bank of Japan
989:DNA Data Bank of Japan
636:10.1093/molbev/msaa316
328:Variants of SARS-CoV-2
1482:Computational biology
997:Secondary databases:
53:; 4 years ago
979:Sequence databases:
187:South Cambridgeshire
1275:Whitehead Institute
1063:Rat Genome Database
572:Nature Microbiology
471:Nature Microbiology
279:Lineage assignation
249:Lineage designation
32:
1512:Sequence alignment
1219:Flatiron Institute
877:pangolin.cog-uk.io
398:10.1093/ve/veab064
51:30 April 2020
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1507:Sequence database
1021:Protein Data Bank
1015:Other databases:
478:(11): 1403–1407.
255:phylogenetic tree
238:COVID-19 pandemic
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16:(Redirected from
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42:PANGOLIN logo
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1436:Nexus format
1431:NeXML format
1426:FASTQ format
1421:FASTA format
1409:File formats
1171:Institutions
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885:. Retrieved
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288:Availability
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89:26 July 2023
1416:CRAM format
1337:(CSIR-IGIB)
887:13 February
851:19 November
821:13 February
788:13 February
728:13 February
551:18 February
244:Description
76:4.3.1
1559:Categories
1502:Sequencing
1466:GTF format
1461:GFF format
1456:VCF format
1446:SAM format
1209:(EMBL-EBI)
1135:SOAP suite
1055:VectorBase
1017:BioNumbers
1003:Swiss-Prot
673:22 January
578:(3): 415.
444:22 January
344:References
333:Nextstrain
195:SARS-CoV-2
122:Written in
103:Repository
58:2020-04-30
1329:(ISCB-SC)
1299:(EMBL-AR)
1232:(MPI-CBG)
973:Databases
645:0737-4038
512:220544096
115:/pangolin
1531:Category
1401:(RECOMB)
1351:Meetings
1305:(EMBnet)
1155:Server:
1130:SAMtools
1125:PANGOLIN
1088:Software
1067:PHI-base
1059:WormBase
1029:InterPro
906:pangolin
881:Archived
845:Archived
815:Archived
782:Archived
752:Archived
722:Archived
667:Archived
663:33295605
604:33514928
545:Archived
504:32669681
438:Archived
416:34527285
364:1 August
317:See also
211:pangolin
199:COVID-19
175:PANGOLIN
149:pangolin
18:PANGOLIN
1543:Commons
1378:(InCoB)
1323:(ISCB)
1311:(INSDC)
1293:(ASBCB)
1197:(DBCLS)
1191:(COSBI)
1105:Clustal
1051:FlyBase
1025:Ensembl
999:UniProt
981:GenBank
758:4 March
691:bioRxiv
654:7798932
595:7845574
495:7610519
407:8344591
217:Context
151:.cog-uk
144:Website
133:License
87: (
56: (
1384:(CIBB)
1372:(ISMB)
1366:(ECCB)
1343:(JSBi)
1249:(NBIC)
1238:(NCBI)
1226:(JCVI)
1215:(EMBL)
1203:(DDBJ)
1157:ExPASy
1140:TopHat
1120:MUSCLE
1110:EMBOSS
1100:Bowtie
1075:GISAID
1035:, and
1007:TrEMBL
910:GitHub
693:
661:
651:
643:
602:
592:
510:
502:
492:
414:
404:
260:GitHub
207:GISAID
156:
126:Python
109:github
1395:(PSB)
1317:(ISB)
1266:(SIB)
1255:(PGC)
1185:(CBD)
1149:Other
1115:HMMER
1095:BLAST
508:S2CID
338:INSDC
310:Lab.
298:Conda
1077:and
1043:BOLD
1033:KEGG
1009:and
991:and
889:2021
853:2021
823:2021
790:2021
760:2021
730:2021
675:2021
659:PMID
641:ISSN
600:PMID
553:2021
500:PMID
446:2021
412:PMID
366:2023
193:for
169:The
111:.com
908:on
649:PMC
631:doi
590:PMC
580:doi
490:PMC
480:doi
402:PMC
394:doi
185:in
153:.io
1561::
1360:()
1073:,
1069:,
1065:,
1061:,
1057:,
1053:,
1049:,
1045:,
1031:,
1027:,
1023:,
1019:,
1005:,
987:,
983:,
879:.
875:.
864:^
855:.
843:.
839:.
813:.
809:.
798:^
780:.
776:.
750:.
746:.
720:.
716:.
699:.
665:.
657:.
647:.
639:.
627:38
625:.
621:.
598:.
588:.
574:.
570:.
539:.
520:^
506:.
498:.
488:.
474:.
468:.
454:^
436:.
432:.
410:.
400:.
388:.
384:.
240:.
213:.
958:e
951:t
944:v
891:.
825:.
792:.
762:.
732:.
677:.
633::
606:.
582::
576:6
555:.
514:.
482::
476:5
448:.
418:.
396::
390:7
368:.
173:(
91:)
60:)
20:)
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