Jalview is a piece of

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

software that is used to look at and edit

multiple sequence alignment Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis an ...

s. The program was originally written by Michele Clamp whilst working in Geoff Barton's group at the

University of Oxford The University of Oxford is a collegiate university, collegiate research university in Oxford, England. There is evidence of teaching as early as 1096, making it the oldest university in the English-speaking world and the List of oldest un ...

and

European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wel ...

(EBI). Jalview 2, a re-engineered version produced by Andrew Waterhouse and Jim Procter whilst working in Geoff Barton's group at the School of Life Sciences,

University of Dundee The University of Dundee is a public research university based in Dundee, Scotland. It was founded as a university college in 1881 with a donation from the prominent Baxter family of textile manufacturers. The institution was, for most of its ...

, was released in 2005, and its development is supported by the

Biotechnology and Biological Sciences Research Council Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds science, scient ...

(BBSRC) and

Wellcome Trust The Wellcome Trust is a charitable foundation focused on health research based in London, United Kingdom. It was established in 1936 with legacies from the pharmaceutical magnate Henry Wellcome (founder of Burroughs Wellcome, one of the predec ...

. It is used widely by a variety of web servers (e.g. the EBI ClustalW server and the

Pfam Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. It is cur ...

protein domain database) but is also available as a general purpose alignment editor. Jalview has a wide range of functions in addition to multiple sequence alignment generation, viewing and editing, including calculating

phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

s and viewing molecular structures. Recent versions of Jalview include features for the analysis of genetic variation from public databases or local

Variant Call Format The Variant Call Format or VCF is a standard text file format used in bioinformatics for storing gene sequence or DNA sequence variations. The format was developed in 2010 for the 1000 Genomes Project and has since been used by other large-sca ...

(VCF) files. Jalview connects to many external

web services A web service (WS) is either: * a service offered by an electronic device to another electronic device, communicating with each other via the Internet, or * a server running on a computer device, listening for requests at a particular port over a n ...

to import data and perform calculations.

References

{{Reflist Phylogenetics software Genetics in the United Kingdom Science and technology in Cambridgeshire South Cambridgeshire District

See also

References