Jalview

The Jalview Java alignment editor. Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments.


References in zbMATH (referenced in 10 articles )

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  2. Jones, Martin O.; Koutsovoulos, Georgios D.; Blaxter, Mark L.: Iphy: an integrated phylogenetic workbench for supermatrix analyses (2011) ioport
  3. Guerra-Assunção, José Afonso; Enright, Anton J.: Mapmi: automated mapping of microrna loci (2010) ioport
  4. Ilinkin, Ivaylo; Ye, Jieping; Janardan, Ravi: Multiple structure alignment and consensus identification for proteins (2010) ioport
  5. Jankun-Kelly, T. J.; Lindeman, Andrew D.; Bridges, Susan M.: Exploratory visual analysis of conserved domains on multiple sequence alignments (2009) ioport
  6. Waterhouse, Andrew M.; Procter, James B.; Martin, David M. A.; Clamp, Michele E.; Barton, Geoffrey J.: Jalview version 2 - a multiple sequence alignment editor and analysis workbench (2009) ioport
  7. Caffrey, Daniel R.; Dana, Paul H.; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E.; Somaroo, Shyamal; Caffrey, Brian E.; Potluri, Shobha; Huang, Enoch S.: PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments (2007) ioport
  8. Jiang, Haiyan; Blouin, Christian: Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions (2007) ioport
  9. Nebel, Jean-Christophe; Herzyk, Pawel; Gilbert, David R.: Automatic generation of 3D motifs for classification of protein binding sites (2007) ioport
  10. Prlić, Andreas; Down, Thomas A.; Kulesha, Eugene; Finn, Robert D.; Kähäri, Andreas; Hubbard, Tim Jp: Integrating sequence and structural biology with DAS (2007) ioport