I wonder if someone can help me with $subject ; I've never done such work although I'm a biologist and programmer. I'd like to know what software, preferably open source, is used to taxonomically rank DNA/Protein sequences. Ideally commandline building blocks (for making a pipeline). I've worked with GenBank and UniProt data before but mostly to provide annotation to experimental data. Perhaps there are review papers that I could look at? Or point me at papers where results really are repeatable from the supplementary data/info ? - thanks
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