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 72517 leaves and 66153 forking nodes (and 0 monotypic nodes).

The input cleaned taxonomy had 2641298 leaves and 133838 forking nodes (and 80892 monotypic nodes).

2568781 leaves were added to create the solution. 4447 taxa were rejected.

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

• the ./labelled_supertree.tre (full solution with names 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