Jalview is a multiple sequence alignment

Multiple sequence alignment

A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...

 editor and viewer written in the Java programming language

Java (programming language)

Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

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

European Bioinformatics Institute

The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...

.. Jalview 2, a re-engineered version produced by Andrew Waterhouse and Jim Procter whilst working in Geoff Barton's group at the University of Dundee

University of Dundee

The University of Dundee is a university based in the city and Royal burgh of Dundee on eastern coast of the central Lowlands of Scotland and with a small number of institutions elsewhere....

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

Biotechnology and Biological Sciences Research Council

Biotechnology and Biological Sciences Research Council is a UK Research Council and NDPB and is the largest UK public funder of non-medical bioscience...

.

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

European Bioinformatics Institute

The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...

 ClustalW server and the Pfam

Pfam

Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.- Features :For each family in Pfam one can:* Look at multiple alignments* View protein domain architectures...

 protein domain database) but is available as a general purpose alignment editor.


Jalview has a wide range of functions in addition to multiple sequence alignment viewing and editing including calculating phylogenetic tree

Phylogenetic tree

A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...

s and viewing molecular structures. Many of these use external web services to import data.