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

The subproblems directory holds the 2 subproblems. Each one is a slice of the full tree. They do not overlap. The decomposition is produced by identifying each higher taxon that is not contested by any single phylogenetic input. This taxon becomes the root of the subproblem (and is used in the file name to identify the subproblem). Many of the subproblems contain only trivial phylogenetic statements. See the subproblems README for details on the procedure.

Next step: Solving the subproblems. See ../subproblem_solutions/index.html for details.

Results: This page contains the list of subproblems, the list of subproblems overlapping each input tree, and the list of contested taxa.

List of subproblems

Each of the 2 subproblems is a list of trees (in newick representation) with the order reflecting the ranking of the input trees. The taxonomy overlaps with every subproblem.

Sorted by the number of phylogenetic inputs, the subproblems are:

Subproblem# inputs# tipsInput Identifiers
ott5268475.tre 3 2 xx_1@1.tre, xx_2@1.tre, TAXONOMY
ott805080.tre 3 2 xx_1@1.tre, xx_2@1.tre, TAXONOMY

Overlap between trees and subproblems

The list of input phylogenetic trees sorted by the number of subproblems that they overlap with is:

Study+Tree key# subproblemsSubproblem Identifiers
xx_2@1 2 ott5268475, ott805080
xx_1@1 2 ott5268475, ott805080

Contested taxa

The 0 contested taxa follow. For each taxon, we list the input tree(s) that conflict with the taxon. For each tree, the "parent nodes" are internal nodes each of which has at least 1 child that belongs entirely to the taxon and at least one descendant that does not belong in the taxon. If the OTT Id were not contested, there would only be one internal node that fit those criterion, but in contested taxa there are multiple.