This folder structure contains the output of the pipeline in accordance with the configuration specified in the corresponding code release, which in a local install can be found in ../config/config.yaml
The subfolder structure is organized as follows:
databases contains the aggregated SQLite database with barcodes,
BOLD taxonomy information reconciled with the Open Tree of Life, and the topology
of the open tree. Any zero-byte files with the *.ok extension that are in this
folder can be ignored as they functioned as status updates for the various
database update processes.fasta principally contains FASTA multiple sequence files (*.fa) and
Newick tree files (*.tre). These are inputs for RAxML, which produces a number
of output files, all of which will have *.raxml.* in their file names. The files
are organized in families, which are processed in parallel and which are organized
in folders with m-of-n names. The backbone files across families are in the root
of the fasta folder.grafted.tre is the final tree.