Tree file and taxonomy
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5.2 years ago
yuki.weber81 ▴ 10

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.

tree taxonomy mothur • 1.9k views
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5.0 years ago
jhc ★ 2.9k

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/

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