[Jalview-discuss] Jalview applet compatibility issue

vincent ranwez vincent.ranwez at univ-montp2.fr
Mon Dec 12 08:42:56 GMT 2011

Dear Jalview developper's team,

Our team is relying on Jalview applet to display sequence alignments in two projects:
1. OrthoMaM a database of othologuous mammalian molecular markers. The current OrthoMaM release (v6) is based on EnsEMBL v56. It now includes 6,056 exons and 12,777 CDS alignments for up to 36 species (http://www.orthomam.univ-montp2.fr/)
2. MACSE  an automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. MACSE has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence (http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=macse)

We are really pleased with Jalview functionality's but it seems that the applet as compatibility issues. Indeed the applet is not loaded with JRE1.5 and the following web browser:
chrome 15.0.874.121, firefox 8.0.1, safari 5.0.5 

We encounter the same compatibility issues on the demo page of your web site : http://www.jalview.org/examples/embedded.html

It seems that the standard way to include embedded applet is now to rely on .class files. The last jalview release (2.7) does not provide such files, can you please provide those files or alternative solutions so that we can continue to benefit from your JalView applet.

sincerely yours,


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