Brian Ondov

Hi Lee- I think the closest thing available is adding GET variables to the URL, e.g.: http://marbl.github.io/Krona/examples/phymmbl.krona.html?font=15 If that works for you, the best way to see what's available is...

Definitely! The code is not well documented but I can try to walk you through anything that doesn't make sense.

Sure, anything through the command line would pretty much have to alter the XML spec. It should stay backwards compatible as long as we're just adding things though.

I can answer any questions about the code or architecture as needed. @khyox do you want to propose the xml changes here, and if it works for @lskatz move forward...

That's right. More specifically, `dataHeader()`, called from `writeTree()`. You can see there is already a `collapse` option that functions more or less how we want, but is not exposed to...

It is sketching all the reads together, but the first file is used for the ID and comment (see `-I` and `-C`). To create separate sketch files for each read...

Hi @aderzelle, The Krona BLAST classification algorithm is based on LCA (Lowest Common Ancestor), so if your reads have good hits to a diversity of taxa, that would explain the...

It's actually the bit scores that matter rather than e-values, at least by default in recent versions. I'm guessing there are exact ties. You can see what is tying by...

That makes sense, although it's still odd that `-r` made no difference...it may be worth it to check out some of the tax IDs that are tied to see if...

Yes, and in this case, at least, the "uncultured bacteria" hit happens to be the best one, which is why changing the threshold didn't help. I'm not sure what to...