Jalview

Viewer and editor for multiple sequence alignments

Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages e.g. the EBI Clustalw server and the Pfam protein domain database and is also available as a general purpose alignment editor.

o Reads and writes alignments in a variety of formats o Gaps can be inserted/deleted using the mouse. o Group editing insertion deletion of gaps in groups of sequences. o Removal of gapped columns. o Align sequences using Web Services Clustal, Muscle… o Amino acid conservation analysis similar to that of AMAS. o Alignment sorting options by name, tree order, percent identity, group. o UPGMA and NJ trees calculated and drawn based on percent identity distances. o Sequence clustering using principal component analysis. o Removal of redundant sequences. o Smith Waterman pairwise alignment of selected sequences. o Web based secondary structure prediction programs JNet. o User predefined or custom colour schemes to colour alignments or groups. o Sequence feature retrieval and display on the alignment. o Print your alignment with colours and annotations. o Output alignments as HTML pages, images PNG or postscript EPS.