Propinquity output documentation. The top-level docs are here.
The bumped_ott directory a copy of the version of OTT that may have some extinct (often incertae sedis) taxa moved toward the root of the tree.Next step: Choose exemplars for tips in phylogenies that are mapped to higher taxa. See ../exemplified_phylo/index.html.
If there is an
"edits" property in the JSON
file at ../cleaned_ott/move_extinct_higher_log.json.
If that property does not exist, then the taxonomy files in this directory
will be links to the files in ../subott_dir.
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.
The taxonomic structure in the files in this directory will determine the phylogenetic interpretation of names in the rest of the synthesis run.