MSI Galaxy has been updated to the Oct 23, 2012 Distribution. Details for all recent updates are at: http://wiki.g2.bx.psu.edu/DevNewsBriefs
Among recent changes are improvements and additions to galaxy visualization:
A few recent tools additions of note:
The tuxedo tools: bowtie, tophat, and cufflinks, are now available at version 2
CummeRbund - provides visualizations for the results of Cuffdiff
MetaPhlAn - (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
SnpEffect - a variant annotation and effect prediction tool annotates and predicts the effects of variants on genes (such as amino acid changes).