paired samples

[Stef]

Dear Lefse developers,

Thanks for a great tool! I really like the visualisation as well. 

I have a few questions:

1. Most important: I have paired data, i.e. samples from x different subjects taken before and after an intervention. How can I run a PAIRED wilcoxon in lefse?

2. How can I change colors in the output?

3. In the cladogram, how can I get a legend down to species level? Somehow I only get family level.

Thanks a lot for your help!

/Stef