Thanks for the detailed breakdown of the places to check, Carl! I was able to fix the issue following the steps you've outlined. For the benefit of other readers, here is what I did to fix it:

On Tue, Jan 26, 2016 at 10:09 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hi, Oksana

There are a few places to look and things to check in this situation.

First, are other visualizations working on your production instance? Do you see the visualization icon/button and does the dropdown there have the 'charts' visualization on tabular files (like bed)?

Yes, I am able to see other visualizations.
 

On the admin side for this, when your instance starts up you should see a section of logging data for visualizations that are loaded or error in the paster log. They're shown after the converter tools output logging info and before the job runners output theirs. They look something like:

galaxy.web.base.pluginframework INFO 2016-01-26 09:57:37,989 VisualizationsRegistry, loaded plugin: phyloviz

You should see the standard visualizations load there including 'phyloviz'. If there's a problem, then you'll see a stack trace and a message saying that it was skipped.

Logs where showing no problems.
 

Second, if visualizations are working well for other types, can you try uploading a phyloxml file and seeing if phyloviz will launch from that data? There's an example in this history: 

https://test.galaxyproject.org/u/carleberhard/h/phyloviz

Uploaded phyloxml sample and it was showing visualization icon.
 

Third, it may be an issue with how the datatype is being referenced in the phyloviz config file (when compared with your datatypes_conf.xml file).

I've checked datatypes_conf.xml file and the lines that describe newick and nexus datatypes where commented out. A bit silly, but that was what was breaking it. Uncommenting them fixed the issue.

Thanks for all your help, guys!

Cheers,
Oksana