Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Graph of Life Commander
Python
branch: master
Failed to load latest commit information.
example minor
files_for_submission_v1.0 more
files_for_submission_v2.0 v2.0 files
misc small movements
taxa_viz fixed viz bits
.gitignore all
CONTRIBUTORS Add LICENSE and CONTRIBUTORS files
LICENSE Add LICENSE and CONTRIBUTORS files
New_studies-microbes.py file update
New_studies.py update files
README.md Update README.md
aln_reader.py more
aln_utils.py more
collect_study_ids.py correction of file extension
convert_tree_to_taxonomy.py some work
create_mapped_taxa_taxonomy_tree.py small changes
delete_knees.py minor changes
general_tm_utils.py download nexsons from api instead of devapi
general_utils.py more
get_name_info.py more files
load_mls.py some files
load_mls_JWB.py update files
load_mrp.py more
load_studies.py small changes
load_studies_JWB.py minor
load_studies_inf_mono.py plants added
load_studies_inf_mono_JWB.py update files
load_synth_extract.py some files
load_taxonomy.py minor change
mapped_taxa added mapped taxa
mls_posttree_fix.py fixing mls
node.py viz
process_taxa_from_test_studies.py more edits
process_taxonomy_for_load_log.py tax
process_tree_log_load.py small changes
process_tree_log_load_get_number_tips.py small changes
process_tree_log_load_get_scope.py small changes
run_JWB.py update files
run_Plants.py synth files
run_asterales_example.py adding option to specify location of treemachine jar
run_synth_studies_mono.py Files for submission.
seq_reader.py more
sequence.py more
stephen_laptop_conf.py fix taxonomy
subset_taxonomy.py small update
synth_one_tree.py inf mono
synth_studies.py synth files
taxonomy_tree_export.py some work
test_concat.py more
test_studies.py minor changes
tree_reader.py first real commit
tree_utils.py some work
wopr_conf.py minor JWB files

README.md

gcmdr

Graph of Life Commander

This repo contains scripts for loading trees into treemachine, as well as lists of studies currently being incorporated into the synthetic tree.

If you want the most up-to-date list of studies being incorporate, run the collect_input_trees.pl script. This checks the taxon files listed in life.py and extracts the tree identifiers from each taxon file. Alternately, look at the list of imports in life.py (for example 'from microbes import studytreelist as microbelist'. The microbes.py file would contain a list of the microbe trees, usually with comments containing a short citation.

Files

Files with taxon names (fungi.py, birds.py, etc) contain study lists for import. Studies listed in """…""" comments are those that have been requested for synthesis but have not yet passed all of the import checks.

  • collect_input_studies.py: prints a list of the json files that are currently being synthesized into the draft tree
  • get_name_info.py: ultilty script to get information about a name from treemachine
  • life.py: loads all of the studies into treemachine (imports other taxon_name.py files)
  • tree_utils.py: create consensus trees, calculate bipartitions, calculate distances

Tree identifiers

Within the lists found in the taxon files, trees (usually only one per study) are designated as "MMM_NNN" where MMM is the study id and NNN is the id of a tree within that study.

Something went wrong with that request. Please try again.