jalview-2.07_2.txz


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Description

jalview - Viewer and editor for multiple sequence alignments

Property Value
Distribution FreeBSD 12
Repository FreeBSD Ports Quarterly i386
Package filename jalview-2.07_2.txz
Package name jalview
Package version 2.07
Package release 2
Package architecture i386
Package type txz
Category biology java
Homepage http://www.jalview.org
License -
Maintainer ports@FreeBSD.org
Download size 5.57 MB
Installed size 6.27 MB
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
===>   NOTICE:
The jalview port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:
https://bugs.freebsd.org/bugzilla
More information about port maintainership is available at:
https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

Alternatives

Package Version Architecture Repository
jalview-2.07_3.txz 2.07 i386 FreeBSD Ports Latest
jalview-2.07_3.txz 2.07 amd64 FreeBSD Ports Latest
jalview-2.07_2.txz 2.07 amd64 FreeBSD Ports Quarterly
jalview - - -

Requires

Name Value
openjdk8 = 8.202.8

Download

Type URL
Mirror pkg.freebsd.org
Binary Package jalview-2.07_2.txz
Source Package biology/jalview

Install Howto

Install jalview txz package:

# pkg install jalview

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