mirror of
https://git.FreeBSD.org/ports.git
synced 2024-12-16 03:24:07 +00:00
26 lines
1.3 KiB
Plaintext
26 lines
1.3 KiB
Plaintext
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) and is also available as a general purpose alignment editor.
|
|
|
|
o Reads and writes alignments in a variety of formats
|
|
o Gaps can be inserted/deleted using the mouse.
|
|
o Group editing (insertion deletion of gaps in groups of sequences).
|
|
o Removal of gapped columns.
|
|
o Align sequences using Web Services (Clustal, Muscle...)
|
|
o Amino acid conservation analysis similar to that of AMAS.
|
|
o Alignment sorting options (by name, tree order, percent identity, group).
|
|
o UPGMA and NJ trees calculated and drawn based on percent identity distances.
|
|
o Sequence clustering using principal component analysis.
|
|
o Removal of redundant sequences.
|
|
o Smith Waterman pairwise alignment of selected sequences.
|
|
o Web based secondary structure prediction programs (JNet).
|
|
o User predefined or custom colour schemes to colour alignments or groups.
|
|
o Sequence feature retrieval and display on the alignment.
|
|
o Print your alignment with colours and annotations.
|
|
o Output alignments as HTML pages, images (PNG) or postscript (EPS).
|
|
|
|
If you use Jalview in your work, please quote this publication. Clamp, M., et
|
|
al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7
|
|
|
|
WWW: http://www.jalview.org
|