Propinquity output documentation. The top-level docs are here.
The subott_dir directory a copy of the version of OTT that is rooted at the root of this synthesis run. After this subtree of the OTT is produced, it is used as the OTT for the remainder of the synthesis run for the sake of performance.
See https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Interim-taxonomy-file-format for documentation of the OTT format.
*.pickle files are Python pickle artifacts of reading the taxonomy. They can be deleted because they can be regenerated from the primary OTT files.