There are many ways to do it. But for almost all of them, the sequence names will have to be created with labels that will then be used to color each OTU by some aspect of the name.

The Interactive Tree of Life project is one good resource:

https://itol.embl.de/

The HIV Databases at LANL provides another simple tree coloring service:

https://www.hiv.lanl.gov/content/sequence/RAINBOWTREE/rainbowtree.html

The Augur and Auspice tools are also very helpful:

https://docs.nextstrain.org/en/latest/learn/augur-to-auspice.html

In Figtree, you can select individual OTUs, groups of OTUs based on a character set in the names, or select clades, and then color the brnaches, the OTU names, or both.

http://tree.bio.ed.ac.uk/software/figtree/

Brian Thomas Foley

Thank you Brian. Your answer was so helpful

Hi! Try the ggtree package in R.

Thank you Yanjing Wang