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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
Viewer and editor for multiple sequence alignments

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 13 Feb 2006 09:43:01
Also Listed In: java
License: not specified in port


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
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.

Required To Build:
  1. java/openjdk6
  2. devel/apache-ant
Required To Run:
  1. java/openjdk6
There are no ports dependent upon this port

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


Configuration Options
     No options to configure

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

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
21 Jan 2014 23:18:05
Original commit files touched by this commit  2.07_2
Revision:340671
bapt search for other commits by this committer
Fix properties on pkg-plist
20 Jan 2014 23:10:11
Original commit files touched by this commit  2.07_2
Revision:340487
bapt search for other commits by this committer
Support stage
20 Sep 2013 15:55:44
Original commit files touched by this commit  2.07_2
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
10 Dec 2012 11:25:28
Original commit files touched by this commit  2.07_2
Revision:308600
bapt search for other commits by this committer
Decommissioning java 1.5 (EOLed since October 2009):
suppress any reference to USE_JAVA=	1.5+ (part1)
01 Oct 2012 14:45:17
Original commit files touched by this commit  2.07_2
Revision:305130
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
21 Jul 2011 05:03:02
Original commit files touched by this commit  2.07_2
linimon search for other commits by this committer
Now that the Java 1.3 and Java 1.4 ports are deprecated and will expire soon,
remove support for them from bsd.java.mk.  As Jikes is not available in Java 1.5
or higher, remove it from bsd.java.mk too (suggested by hq@) and from the ports
which used it (only occurences were USE_JIKES=no).  Support for the Blackdown VM
is also removed, as it is not available in Java 1.5 and higher.

Also remove the mapping from Java 1.1-1.4 to Java 1.5+ in bsd.java.mk to detect
old, broken ports; therefore bump the minimal value of JAVA_VERSION to 1.5.
While here, replace static values of JAVA_VERSION in files/*.in by
%%JAVA_VERSION%% .

PR:             ports/158969
Submitted by:   rene
Tested on:      pointyhat-west -exp
19 Mar 2011 12:38:54
Original commit files touched by this commit  2.07_2
miwi search for other commits by this committer
- Get Rid MD5 support
06 Jun 2008 13:08:29
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 20:32:57
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: 10

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