The files in this directory (and its children) were produced using propinquity, a snakemake-based pipeline for phylogenetic supertrees.

Configuration

The configuration file for the propinquity run is at config.json. The run completed at 2024-05-30 16:51:14.

Taxonomy

• OTT version: 3.7 (specifically version 3.7draft2)
• root taxon: 93302 (cellular organisms)
• The local copy of this version of OTT was at /home/mholder/ot2023/ott/ott3.7.2
• This version of OTT was pruned to removed taxa that are flagged with any of the following taxon flags:
  • barren
  • environmental
  • hidden
  • hybrid
  • inconsistent
  • major_rank_conflict
  • major_rank_conflict_inherited
  • merged
  • not_otu
  • viral
  • was_container

Phylogenetic inputs

The phylesystem shards for this run were located under /home/mholder/ot2023/phylesystem

The collections shards for this run were located under /home/mholder/ot2023/phylesystem. 11 collections were used, ranked in this order:

1. pcart/cnidaria
2. mwestneat/reef-fishes
3. josephwb/hypocreales
4. kcranston/catfish
5. kcranston/barnacles
6. opentreeoflife/plants
7. josephwb/aves
8. opentreeoflife/metazoa
9. opentreeoflife/fungi
10. opentreeoflife/safe-microbes
11. opentreeoflife/default

Tools

otcetera

• version: 0.0.01-dev and git SHA 10d935ef9eaacc1bb2f9c357c9df7c6030628176
• compiled using version 1_74 of the boost C++ libraries

peyotl

• version: 1.0.2dev

propinquity

• git SHA unknown

Processing of phylogenetic inputs

1. phylo_input/index.html discusses the list of 1,362 input phylogenetic trees that were identified from the collections.
2. phylo_snapshot/index.html links to the git SHA of these trees and copies of them as they existed when the supertree pipeline was run.
3. cleaned_phylo/index.html describes the pruning of tips from input phylogenies due to mapping to problematic taxa. There were 1338 nonempty trees after that cleaning.
4. exemplified_phylo/index.html describes the choice of terminal taxa to exemplify those nodes that are mapped to higher taxa.

Processing of taxonomic inputs

1. The subott_dir directory holds a version of the OpenTree Taxonomy pruned so that the root taxon is 93302.
2. The cleaned_ott directory holds information from the removal of flagged taxa and pruning to the chosen root.
3. The bumped_ott directory holds a version of the OpenTree Taxonomy that may have some incertae sedis taxa moved toward the root of the tree. This is done to make the movement of taxonomically uncertain groups less disruptive to the taxonomic naming steps.
4. exemplified_phylo/index.html describes how the choice of exemplars for the phylogenetic inputs also leads to a pruned taxonomy with these exemplars.

Supertree algorithm

1. subproblems/index.html describes the decomposition of the full tree into adjacent subproblems. For the sake of comparison, a version of the subproblems with the order of phylogenetic inputs reversed may be generated at reversed_subproblems/index.html
2. subproblem_solutions/index.html describes the solutions that result from each of these subproblems. If the reversed subproblems were produced, their solutions will be in reversed_subproblem_solutions/index.html.
3. grafted_solution/index.html describes piecing the subproblem solutions into a single solution for the exemplified taxa.
4. labelled_supertree/index.html describes how the taxa pruned off in the exemplar step are reattached to produce a full supertree.

Annotation of the supertree

See annotated_supertree/index.html links to the annotations for that tree.

Assessment of the pipeline

See assessments/index.html discusses what tests were run to assess the supertree.

Final output

1. ./labelled_supertree/labelled_supertree.tre (the tree)
2. ./annotated_supertree/annotations.json (the annotations file)