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) but is available as a general purpose
alignment editor.

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

Please Note: this software is a Java Web Start Application, you need to right-click on the download file and choose "Launch".

Requirements:
* Java
* Internet Connection

The license of this software is Freeware, you can free download and free use this calculator software.