Jalview 2.7

Jalview - A multiple alignment editor written in Java.

A multiple alignment editor written in Java.

Jalview is used widely in a variety of web pages but is available as a general purpose alignment editor.

Jalview was designed using the Jav aprogramming language and can function on multiple platforms.

Jalview features :

- 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).
- 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).

Requirements:

- Java

Jalview 2.7 is licensed as Freeware for the Windows operating system / platform. Jalview is provided as a free download for all software users (Freeware).