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

Configuration

The configuration file for the propinquity run was at: /Users/karen/Documents/opentreeoflife/synthesis/treeoflife/opentree9.0/config

Taxonomy

• OTT version: 3.0 (specifically version 3.0draft6)
• root taxon: 93302
• The local copy of this version of OTT was at /Users/karen/Documents/opentreeoflife/data/ott/ott3.0draft6
• This version of OTT was pruned to removed taxa that are flagged with any of the following taxon flags:
  • barren
  • environmental
  • extinct
  • extinct_inherited
  • hidden
  • hybrid
  • inconsistent
  • major_rank_conflict
  • major_rank_conflict_inherited
  • merged
  • not_otu
  • unclassified
  • unclassified_inherited
  • unplaced
  • unplaced_inherited
  • viral
  • was_container

Phylogenetic inputs

The phylesystem shards for this run were located under /Users/karen/Documents/opentreeoflife/data/phylesystem-prod/

The collections shards for this run were located under /Users/karen/Documents/opentreeoflife/data/phylesystem-prod/. 10 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. opentreeoflife/metazoa
8. opentreeoflife/fungi
9. opentreeoflife/safe-microbes
10. opentreeoflife/default

Tools

otcetera

• version: 0.0.01-dev and git SHA e8772e9c
• compiled using version 1_63 of the boost C++ libraries

peyotl

• the filepath of the root directory of peyotl was /Users/karen/Documents/opentreeoflife/software/peyotl
• version: 0.1.4dev and git SHA 33015837feb48b73c96bd858a31e55139addad30

propinquity

• git SHA f69b67fcfc48490282a4f04ad96e378b2db0a35f

Processing of phylogenetic inputs

1. phylo_input/index.html discusses the list of 819 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 811 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.

Logs for these steps are here (stdout) and here (stderr)

Processing of taxonomic inputs

1. cleaned_ott/index.html describes the removal of flagged taxa and pruning to the chosen root.
2. 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.
2. subproblem_solutions/index.html describes the solutions that result from each of these subproblems.
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.

Logs for these steps are here (stdout) and here (stderr)

Annotation of the supertree

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

Logs for these steps are here (stdout) and here (stderr)

Assessment of the pipeline

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

Logs for these steps are here (stdout) and here (stderr)

Logs for the HTML generation steps are here (stdout) and here (stderr)

An index for all of the logs is available here

Final output

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