results

Bactria pipeline results

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.