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. 2017 Mar 1;5:e3058. doi: 10.7717/peerj.3058

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©2017 Redelings and Holder

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

PMC Copyright notice

Each colored pentagon labels a program (blue for otcetera-based tools and red for python scripts in the propinquity or peyotl repository) that performs the important operations in each step; the number before the tool name refers to the section in this paper that describes the operation. The output of each step corresponds to a subdirectory of the propinquity system which will hold the output artifacts for the step. Ovals are resources that are required (OTT and Open Tree’s phylesystem repository). White pentagons are user-controlled inputs.