Jalview

Jalview is a multiple sequence alignment editor & viewer written in the Java programming language. It is used widely in a variety of web pages (e.g. the EBI ClustalW server and the Pfam protein domain database) but is available as a general purpose alignment editor.

Use Jalview for:
*Viewing
**Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)
***Save alignments and associated trees in Jalview XML format.
*Editing
**Gaps can be inserted/deleted using the mouse or keyboard.
**Group editing (insertion deletion of gaps in groups of sequences).
**Removal of gapped columns.
*Analysis
**Align sequences using Web Services (Clustal, Muscle...)
**Amino acid conservation analysis similar to that of AMAS.
**Alignment sorting options (by name, tree order, percent identity, group).
**UPGMA and NJ trees calculated and drawn based on percent identity distances.
**Sequence clustering using principal component analysis.
**Removal of redundant sequences.
**Smith Waterman pairwise alignment of selected sequences.
*Annotation
**Use web based secondary structure prediction programs (JNet).
*Annotation
**User predefined or custom colour schemes to colour alignments or groups.
**Sequence feature retrieval and display on the alignment.
*Publishing
**Print your alignment with colours and annotations.
**Create HTML pages.
**Output alignment as portable network graphics image (PNG).
**Output alignment as encapsulated postscript file (EPS).