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This is the top-level repository in the Open Tree of Life phylogenetic study document store. The data are actually stored in different repositories referred to as "shards" in much of our documentation/email discussions.

If you want to browse the data in phylesystem, you can look at the repository for the only shard. The repo is at If you want to find study ot_WXYZ you should look in study/ot_YZ/ot_WXYZ/ot_WXYZ (in other words, in the study subdirectory look in the directory named using the study's prefix ("ot_" or "pg_") followed by the last 2 digits of the ID. In that directory there will be a subdirectory that corresponds to the study ID. and the JSON file will be in that directory.

Phylesystem serves as a crude database storage for the web services implemented using the code base phylesystem-api. This layer is the API for accessing the NexSON data store.

Currently we do not support pull requests to the shards. The server running the NexSON services API is the only writer. We hope to add functionality to smoothly deal with pull requests soon.

See our publication on phylesystem for details. See the germinator repository's wiki for Open Tree of Life documentation.


Most users will only want/need to run the

$ bash pull-studies.bash

script to fetch and pull the latest NexSON for all of the shards


The repository formerly known as phylesystem was moved to: before the current architecture was decided. That repository has a set of files that agree with the intial commit to the phylesystem-1 repo; and it had scripts for updating from phylografter


The code in this repository is released under the 2-clause BSD license. See the LICENSE file for more details.

The data in this repository is released under the Create Commons Zero 1.0 Universal license.


phylogenetic study document storage used by Open Tree of Life




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