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webPRANK is a multiple sequence alignment (MSA) tool for DNA, protein, cDNA, and codon sequences at Goldman Group (EBI). It has structure models built-in and includes a web-based visualization of multiple alignments.


Phylogeny; Sequence analysis; Nucleic acid sites, features and motifs; Nucleic acid structure analysis; Sequence sites, features and motifs


  • Operation: Visualization; Multiple sequence alignment
  • Input: FASTA; Newick
  • Output: FASTA
  • Software interface: Web user interface
  • Language: C++
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Other
  • Cost: Free
  • Version name: -
  • Maturity: Stable
  • Credit: Wellcome Trust [Programme Grant GR078968].
  • Contact: webprank _at_;ari _at_;ari.loytynoja _at_
  • Collection: EBI Tools


Löytynoja A, Goldman N "webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser." BMC Bioinformatics. 2010 Nov 26;11:579.
PMID: 21110866
PMCID: PMC3009689

Madeira F, Madhusoodanan N, Lee J, Tivey ARN, Lopez R "Using EMBL-EBI Services via Web Interface and Programmatically via Web Services." Curr Protoc Bioinformatics. 2019 Apr 30:e74.
PMID: 31039604

Harte N, Silventoinen V, Quevillon E, Robinson S, Kallio K, Fustero X, Patel P, Jokinen P, Lopez R "Public web-based services from the European Bioinformatics Institute." Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W3-9.
PMID: 15215339
PMCID: PMC441543

Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R. "SOAP-based services provided by the European Bioinformatics Institute." Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W25-8.
PMID: 15980463
PMCID: PMC1160251

Labarga A, Valentin F, Anderson M, Lopez R. "Web services at the European bioinformatics institute." Nucleic Acids Res. 2007 Jul;35(Web Server issue):W6-11. Epub 2007 Jun 18.
PMID: 17576686
PMCID: PMC1933145

McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R. "Web services at the European Bioinformatics Institute-2009." Nucleic Acids Res. 2009 Jul;37(Web Server issue):W6-10.
PMID: 19435877
PMCID: PMC2703973

Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. "A new bioinformatics analysis tools framework at EMBL-EBI." Nucleic Acids Res. 2010 Jul;38(Web Server issue):W695-9.
PMID: 20439314
PMCID: PMC2896090

McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R "Analysis Tool Web Services from the EMBL-EBI." Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600.
PMID: 23671338
PMCID: PMC3692137

Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R "The EMBL-EBI bioinformatics web and programmatic tools framework." Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4.
PMID: 25845596
PMCID: PMC4489272

Chojnacki S, Cowley A, Lee J, Foix A, Lopez R "Programmatic access to bioinformatics tools from EMBL-EBI update: 2017." Nucleic Acids Res. 2017 Jul 3;45(W1):W550-W553.
PMID: 28431173
PMCID: PMC5570243

Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, Lopez R "The EMBL-EBI search and sequence analysis tools APIs in 2019." Nucleic Acids Res. 2019 Apr 12. pii: gkz268.
PMID: 30976793

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