Comments on: Phylogenetic Placement Revisited https://www.polarmicrobes.org/phylogenetic-placement-revisited/ Marine Microbial Ecology Sat, 17 Dec 2016 00:18:07 +0000 hourly 1 https://wordpress.org/?v=6.9 By: Jeff https://www.polarmicrobes.org/phylogenetic-placement-revisited/#comment-309 Fri, 13 May 2016 19:52:43 +0000 http://www.polarmicrobes.org/?p=917#comment-309 In reply to Jeff.

Actually, you can now check out this post. The paprica wrapper is excellent if you want to dissect it, but it wont’ work on its own outside of the paprica framework.

]]> By: Jeff https://www.polarmicrobes.org/phylogenetic-placement-revisited/#comment-305 Thu, 28 Apr 2016 14:47:19 +0000 http://www.polarmicrobes.org/?p=917#comment-305 If you’re interested in using phylogenetic placement on 16S rRNA gene collections I strongly recommend that you use our paprica-place_it.py wrapper for pplacer included as part of the paprica metabolic inference pipeline instead of the method I describe here. The wrapper reflects the best combination of alignment and tree-building that we’ve been able to come up with, and handles some annoying details (like scrubbing the sequence names of bad punctuation) for you!

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