A 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 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
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
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)
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>
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