jalview 2.07_2 biology =0

A viewer and editor for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar
Port Added: 13 Feb 2006 09:43:01
Also Listed In: java

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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

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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Required To Build: java/diablo-jdk15, devel/apache-ant
Required To Run: java/diablo-jdk15

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To install the port: cd /usr/ports/biology/jalview/ && make install clean
To add the package: pkg_add -r jalview

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Configuration Options

     No options to configure

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Master Sites:

http://www.jalview.org/source/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

Bump portrevision due to upgrade of devel/gettext.

The affected ports are the ones with gettext as a run-dependency
according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT
in Makefile (29 of them).

PR:             ports/124340
Submitted by:   edwin@
Approved by:    portmgr (pav)

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

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.

WWW: http://www.jalview.org

PR:             93054
Submitted by:   Fernan Aguero <fernan@iib.unsam.edu.ar>

10 vulnerabilities affecting 29 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities