Tree file and taxonomy

Question

[yuki.weber81]

Hi there, I'm just setting up my first sequence processing pipeline with mothur. I was able to generate tree files with sequence names as labels. How can I substitute the sequences with taxonomy? Or is there a way to directly generate trees with taxonomic information?

Thanks for your suggestions, Yuki.

Answer 1

[jhc]

If you have access to the taxID of each sequence, you could annotate trees using ete3: http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html#automatic-tree-annotation-using-ncbi-taxonomy

check also the ete-ncbiquery and ete-annotate command line tools: http://etetoolkit.org/documentation/ete-ncbiquery/