Science Score: 33.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov, plos.org -
✓Committers with academic emails
2 of 6 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.8%) to scientific vocabulary
Keywords from Contributors
Repository
Automated taxonomy decoration onto a tree
Basic Info
- Host: GitHub
- Owner: biocore
- License: bsd-3-clause
- Language: Python
- Default Branch: master
- Size: 297 KB
Statistics
- Stars: 15
- Watchers: 6
- Forks: 10
- Open Issues: 11
- Releases: 2
Metadata Files
README.md
tax2tree
[
tax2tree assists in decorating an existing taxonomy onto a phylogenetic tree with overlapping tip names.
An example test tree and input consensus set can be found in tests/data. Once tax2tree is installed and paths are setup appropriately (see INSTALL), you can run the following to reproduce the output seen in Figure 1 in McDonald et al. 2011.
$ t2t decorate -t tests/data/test_consistency.ntree -m tests/data/test_consistency.cons -o test_output
Additional methods
tax2tree provides support for decorating a backbone within .jplace.
$ t2t decorate --placement <path> ...
When decorating a taxonomy where many lineages are represented by individual tips, you can add "nameholders" to the tree. This works by creating a node with zero branch length as the parent of each tip, providing an internal node for a given label. The classic tax2tree algorithm cannot place labels on tips, and this provides a workaround.
$ t2t decorate --add-nameholder ...
Following multifurcation placement resolution, it is possible a single node, or multifurcation will have been created on the parent edge of a named internal node. That new internal node is reasonably likely to be of the same clade. To account for this, it is possible to perform a single node promotion to the new internal node. To avoid overpromotion, it is necessary to specify the set of tips which correspond to the placements so that multifurcations can be detected
$ t2t promote-multifurcation ...
Contact information
Daniel McDonald (mcdonadt@colorado.edu)
Owner
- Name: biocore
- Login: biocore
- Kind: organization
- Location: Cyberspace
- Website: http://biocore.github.io/
- Repositories: 76
- Profile: https://github.com/biocore
Collaboratively developed bioinformatics software.
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel McDonald | m****t@c****u | 142 |
| Stefan Janssen | s****n@g****m | 18 |
| eldnahitna | e****a@0****3 | 12 |
| dparks1134 | d****s@g****m | 11 |
| Florent Angly | f****y@g****m | 6 |
| Askars | a****i@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 15
- Total pull requests: 31
- Average time to close issues: about 3 years
- Average time to close pull requests: 3 months
- Total issue authors: 5
- Total pull request authors: 5
- Average comments per issue: 1.0
- Average comments per pull request: 0.9
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- wasade (8)
- donovan-h-parks (2)
- mortonjt (2)
- jairideout (1)
- fangly (1)
Pull Request Authors
- wasade (23)
- donovan-h-parks (3)
- sjanssen2 (2)
- fangly (2)
- qiyunzhu (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 214 last-month
- Total dependent packages: 1
- Total dependent repositories: 1
- Total versions: 2
- Total maintainers: 1
pypi.org: tax2tree
Taxonomy to tree decoration tools
- Homepage: https://github.com/biocore/tax2tree
- Documentation: https://tax2tree.readthedocs.io/
- License: bsd-3-clause
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Latest release: 1.1
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v2 composite
- conda-incubator/setup-miniconda v2 composite
- actions/checkout v2 composite
- actions/setup-python v2 composite
- pypa/gh-action-pypi-publish release/v1 composite