Propinquity output documentation. The top-level docs are here.

The labelled_supertree directory holds the final solution trees, generated by reattaching the parts of the taxonomy which were not covered by any input tree (from ../cleaned_ott/index.html) to the grafted solution (see ../grafted_solution/index.html).

Next step: Annotate the tree; see ../annotated_supertree/index.html

Results

The input grafted solution had 159,925 leaves and 141,868 forking nodes (and 0 monotypic nodes).

The input cleaned taxonomy had 2,385,875 leaves and 140,174 forking nodes (and 83,456 monotypic nodes).

2,225,950 leaves were added in the labelled_supertree step to create the solution. 9,839 taxa were rejected.

The files of interest in this directory are (for large files, the link will download the file):

• the ./labelled_supertree.tre Newick with ott# labels and mrcaott#ott# labels (the latter are created for non-taxonomic internal nodes).
• the ./labelled_supertree_ottnames.tre the same tree with the name_id format for taxa from OTT.
• the ./broken_taxa.json which describes who members of non-monophyletic taxa are spread across the tree.
• the ./input_output_stats.json which describes the size of the tree before and after unpruning the taxonomic content.
• the ./labelled_supertree_out_degree_distribution.txt shows the out-degree frequency distribution for the nodes in the labelled supertree
• the ./labelled_supertree_ottnames_without_monotypic.tre (if the file exists) is a version of labelled_supertree_ottnames.tre without any taxa that have only one child.
• the ./labelled_supertree_simplified_ottnames.tre (if the file exists) is a version of labelled_supertree_ottnames.tre with names simplified to remove characters that cause problems for some clients (using otc-munge-names). The log for this step will be at simplified_ottnames.log
• the ./labelled_supertree_simplified_ottnames_without_monotypic.tre (if the file exists) is a version of labelled_supertree_ottnames_without_monotypic.tre with names simplified to remove characters that cause problems for some clients (using otc-munge-names). The log for this step will be at simplified_ottnames_without_monotypic.log