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Port details
jalview 2.07_2 biology on this many watch lists=0 search for ports that depend on this port
A viewer and editor for multiple sequence alignments
Maintained by: fernan@iib.unsam.edu.ar search for ports maintained by this maintainer
Port Added: 13 Feb 2006 09:43:01
Also Listed In: java


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

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


Configuration Options
     No options to configure

Master Sites:
http://www.jalview.org/source/
ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

Number of commits found: 3

Commit History - (may be incomplete: see CVSWeb link above for full details)
DateByDescription
06 Jun 2008 14:08:29
Original commit files touched by this commit  2.07_2
edwin search for other commits by this committer
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)
19 May 2007 21:32:57
Original commit files touched by this commit  2.07_1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
13 Feb 2006 09:42:13
Original commit files touched by this commit  2.07
hq search for other commits by this committer
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>

Number of commits found: 3

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