Phylogenetic classification: phage

usegalaxy.eu support
1

I would like to use vConTACT2 for phylogenetic classification of some de novo phage genomes as recommended by a colleague. The problem is I cannot seem to find that tool anywhere within the Galaxy EU site. Has it been taken down or am I doing something wrong? Has it perhaps been replaced by a different (hopefully similar) tool? If so, what would the alternative be? Thanks!

2

Welcome @ccox

Would this tool be helpful?

  • pharokka Rapid standardised annotation tool for bacteriophage genomes and metagenomes (link at UseGalaxy.eu)

And we can check with the UseGalaxy.eu administrators to find out of the vConTACT2 tool was ever available and the history. Hi @wm75 what do you think?

Thanks! :slight_smile:

3

Pharokka is the tool I used for annotation. The next step would involve vConTACT2, which would use the output of Pharokka to derive taxonomy. If vConTact2 can be accessed through Galaxy, that would be great. Thanks!

4

Ok, thanks for explaining. I don’t see the other tool and am not current on what may be available for phage genomics specifically. Let’s let the EU get back to us next week since they had some things under development and will know the current status. :slight_smile: