Jalview
From Wikipedia, the free encyclopedia
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.
| Jalview | |
| Developer: | Waterhouse A, Procter J, Barton G, Martin D. (Dundee University) Original Version by Clamp M, Cuff J, Searle S, Barton G |
|---|---|
| OS: | UNIX, Linux, Mac, MS-Windows |
| Use: | Bioinformatics tool |
| Licence: | LGPL |
| Website: | http://www.jalview.org |
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.
- Reads and writes alignments in a variety of formats (Fasta, PFAM, MSF, Clustal, BLC, PIR)
- 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).
