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).