Science Score: 57.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Repository
software for UCE (and general) phylogenomics
Basic Info
- Host: GitHub
- Owner: faircloth-lab
- License: other
- Language: Python
- Default Branch: main
- Homepage: http://phyluce.readthedocs.org/
- Size: 3.96 MB
Statistics
- Stars: 81
- Watchers: 9
- Forks: 51
- Open Issues: 77
- Releases: 4
Metadata Files
README.md
phyluce: software for UCE (and general) phylogenomics
phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.
The package now includes a number of tools spanning:
- the assembly of raw read data to contigs
- the identification of UCE contigs
- parallel alignment generation, alignment trimming, and alignment data summary methods in preparation for analysis
- alignment and SNP calling using UCE or other types of raw-read data.
As it stands, the phyluce package is useful for analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels.
Please see the Documentation for additional information on installing and using phyluce
License
3-clause BSD. See License for more information.
Contributions
phyluce is open-source (see License), and we welcome contributions from anyone who is interested in contributing. To contribute code, please make a pull request on github. The issue tracker for phyluce is also available on github.
Issues
If you have an issue, please ensure that you are experiencing this issue on a supported OS (see Installation) using the conda installation of phyluce. If possible, please submit a test case demonstrating the issue and indicate which platform and which phyluce version you are using.
Citing
If you use the phyluce code in any form, please cite the following manuscripts:
Faircloth BC. 2015. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics. doi: 10.1093/bioinformatics/btv646.
If you are processing UCE data that you have collected by targeted enrichment using our probes/protocols, please also cite the following manuscript, which describes the first use of the general approach:
BC Faircloth, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61: 717–726. doi: 10.1093/sysbio/SYS004.
Owner
- Name: faircloth-lab
- Login: faircloth-lab
- Kind: organization
- Location: Baton Rouge, LA
- Website: http://faircloth-lab.org
- Repositories: 48
- Profile: https://github.com/faircloth-lab
Citation (CITATION.cff)
# YAML 1.2
---
abstract: "Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (<5 Ma to > 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci."
authors:
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affiliation: "Louisiana State University"
family-names: Faircloth
given-names: Brant Chipstead
cff-version: "1.1.0"
doi: "10.1093/bioinformatics/btv646"
message: "If you use this software, please cite it using these metadata."
title: "PHYLUCE is a software package for the analysis of conserved genomic loci"
...
GitHub Events
Total
- Issues event: 31
- Watch event: 3
- Issue comment event: 68
- Push event: 7
- Fork event: 2
Last Year
- Issues event: 31
- Watch event: 3
- Issue comment event: 68
- Push event: 7
- Fork event: 2
Committers
Last synced: about 3 years ago
All Time
- Total Commits: 1,364
- Total Committers: 14
- Avg Commits per committer: 97.429
- Development Distribution Score (DDS): 0.18
Top Committers
| Name | Commits | |
|---|---|---|
| Brant Faircloth | b****t@f****g | 1,118 |
| Brant Faircloth | b****h@g****m | 207 |
| github-actions | g****s@g****m | 23 |
| Lint Action | b****g@f****g | 4 |
| Carl Oliveros | c****s@g****m | 2 |
| Zachary-Muscavitch | 4****h@u****m | 2 |
| The Gitter Badger | b****r@g****m | 1 |
| Caio Raposo | 3****o@u****m | 1 |
| GrahamDB | g****y@g****m | 1 |
| Oleksandr Moskalenko | m****o@u****m | 1 |
| Tobias Andermann | t****n@b****e | 1 |
| Tobias Hofmann | t****n@g****t | 1 |
| milag6 | m****6@g****m | 1 |
| Matthew Kweskin | m****n@u****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 164
- Total pull requests: 4
- Average time to close issues: 3 months
- Average time to close pull requests: about 15 hours
- Total issue authors: 109
- Total pull request authors: 2
- Average comments per issue: 3.55
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 27
- Pull requests: 2
- Average time to close issues: 1 day
- Average time to close pull requests: N/A
- Issue authors: 21
- Pull request authors: 1
- Average comments per issue: 0.63
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jbernst (6)
- louisfnastasi (5)
- brantfaircloth (4)
- hutumpyancha (4)
- alexkrohn (4)
- jb23590 (4)
- luishdez35 (4)
- BirdmanRidesAgain (4)
- marianamazzochi (3)
- Jami5on (3)
- karlyhiggins (3)
- claudiavaga (3)
- bbessesen (3)
- crcardenas (3)
- andreluizherpeto (2)
Pull Request Authors
- stachyris (2)
- Zachary-Muscavitch (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
spack.io: phyluce
phyluce (phy-loo-chee) is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes
- Homepage: https://github.com/faircloth-lab/phyluce
- License: []
-
Latest release: 1.6.7
published almost 4 years ago
Rankings
Maintainers (1)
Dependencies
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- ubuntu 20.04 build
- sphinx_rtd_theme ==3.0.1
- peppercorn *