Which open source software to compute taxonomic distance from open source data (1 Viewer)

[kweetal]

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

 

[THE_FERN]

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

I can give a general answer: more specific requires better understanding what "taxonomically rank" means in this context (+ research by me).

These days R libraries are probably the go-to here, unless you're talking about phylogenetic reconstruction under some complex model. For the latter, you'd turn to custom software, perhaps closed source.