Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
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Found codemeta.json file -
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-
✓Committers with academic emails
1 of 11 committers (9.1%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (17.3%) to scientific vocabulary
Keywords
phylogenetic-analysis
phylogenetics
r
Keywords from Contributors
bioinformatics
Last synced: 9 months ago
·
JSON representation
Repository
Phylogenetic analysis in R
Basic Info
- Host: GitHub
- Owner: KlausVigo
- Language: R
- Default Branch: main
- Homepage: http://klausvigo.github.io/phangorn/
- Size: 136 MB
Statistics
- Stars: 208
- Watchers: 9
- Forks: 41
- Open Issues: 36
- Releases: 3
Topics
phylogenetic-analysis
phylogenetics
r
Created about 12 years ago
· Last pushed 10 months ago
Metadata Files
Readme
Changelog
Contributing
Code of conduct
Codemeta
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
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#' srr-tags-readme
#'
#' @srrstats {G1.1} Addressed existence of other packages/implementations in
#' section on 'Other packages'.
#' @srrstats {EA1.0, EA1.1, EA1.2} Addressed target audience, kinds of data,
#' and kinds of questions addressable through gigs.
```
[](https://cran.r-project.org/package=phangorn)
[](https://cran.r-project.org/package=phangorn)
[](https://cran.r-project.org/package=phangorn)
[](https://github.com/KlausVigo/phangorn/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/github/KlausVigo/phangorn?branch=main)
# phangorn 
phangorn is a package for phylogenetic reconstruction and analysis in the R language. phangorn offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for exploring and comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses.
To get an introduction into phylogenetic inference you want to look at:
```
vignette("Trees", package="phangorn")
```
## Installation
You can install the the latest release `phangorn` of the package from
[CRAN](https://CRAN.R-project.org/package=phangorn), or the development version
from [github](https://github.com/KlausVigo/phangorn) or
[r-universe](https://klausvigo.r-universe.dev/phangorn).
| Type | Source | Command |
|-------------|-----------------|--------------------------------------------------------------|
| Release | CRAN | `install.packages("phangorn")` |
| Development | GitHub | `remotes::install_github("KlausVigo/phangorn")` |
| Development | r-universe | `install.packages('phangorn', repos = 'https://klausvigo.r-universe.dev')` |
To install the development version you may need to install the Biostrings package from bioconductor first:
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biostrings")
```
To use all functionality you might install all you might need to install the
`rgl` and `ggseqlogo` package.
```
install.packages("rgl")
install.packages("ggseqlogo")
```
The development version usually depends on the latest `ape` development
version and information to download can be found
[here](https://emmanuelparadis.github.io/ape_installation.html).
## Citation
If you use phangorn please cite:
Schliep K.P. 2011. phangorn: phylogenetic analysis in R. Bioinformatics, 27(4) 592-593
License
-------
phangorn is licensed under the GPLv2.
Owner
- Name: Klaus Schliep
- Login: KlausVigo
- Kind: user
- Location: Graz, Austria
- Company: Graz University of Technology
- Website: https://ecoevo.social/@KlausSchlp
- Repositories: 82
- Profile: https://github.com/KlausVigo
Senior Scientist at TU Graz
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}GitHub Events
Total
- Issues event: 17
- Watch event: 6
- Delete event: 1
- Issue comment event: 12
- Push event: 199
- Pull request event: 2
- Fork event: 3
Last Year
- Issues event: 17
- Watch event: 6
- Delete event: 1
- Issue comment event: 12
- Push event: 199
- Pull request event: 2
- Fork event: 3
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Klaus Schliep | k****p@g****m | 2,483 |
| iris-bk | o****g@g****m | 11 |
| Martin Smith | m****s@g****m | 5 |
| richelbilderbeek | r****l@r****l | 4 |
| Richel Bilderbeek | r****k | 2 |
| Martin R. Smith | m****h@d****k | 2 |
| Lee Katz | l****z@g****m | 1 |
| Joseph W. Brown | p****b@g****m | 1 |
| Duncan Murdoch | m****n@g****m | 1 |
| Diego Giovane Pasqualin | d****n@g****m | 1 |
| Darío Hereñú | m****a@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 114
- Total pull requests: 27
- Average time to close issues: 5 months
- Average time to close pull requests: 24 days
- Total issue authors: 91
- Total pull request authors: 11
- Average comments per issue: 2.51
- Average comments per pull request: 1.22
- Merged pull requests: 22
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 11
- Pull requests: 3
- Average time to close issues: 2 months
- Average time to close pull requests: 3 days
- Issue authors: 9
- Pull request authors: 2
- Average comments per issue: 0.73
- Average comments per pull request: 0.67
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kbhoehn (7)
- richelbilderbeek (5)
- KlausVigo (5)
- trilisser (3)
- alptaciroglu (3)
- cbird808 (2)
- akhst7 (2)
- wrightaprilm (2)
- jphill01 (2)
- BerzhanKurmanov (2)
- melmasri (2)
- ms609 (2)
- Xinru99 (1)
- ndukler (1)
- iferres (1)
Pull Request Authors
- iris-bk (8)
- KlausVigo (7)
- richelbilderbeek (4)
- ms609 (4)
- thijsjanzen (1)
- kant (1)
- teng-gao (1)
- dwbapst (1)
- lskatz (1)
- josephwb (1)
- dmurdoch (1)
Top Labels
Issue Labels
enhancement (2)
upkeep (1)
Pull Request Labels
Packages
- Total packages: 4
-
Total downloads:
- cran 20,423 last-month
- Total docker downloads: 209,470
-
Total dependent packages: 73
(may contain duplicates) -
Total dependent repositories: 171
(may contain duplicates) - Total versions: 72
- Total maintainers: 1
cran.r-project.org: phangorn
Phylogenetic Reconstruction and Analysis
- Homepage: https://github.com/KlausVigo/phangorn
- Documentation: http://cran.r-project.org/web/packages/phangorn/phangorn.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
-
Latest release: 2.12.1
published over 1 year ago
Rankings
Dependent packages count: 1.3%
Dependent repos count: 1.5%
Forks count: 1.9%
Stargazers count: 2.2%
Downloads: 3.7%
Average: 5.3%
Docker downloads count: 21.0%
Maintainers (1)
Last synced:
10 months ago
proxy.golang.org: github.com/KlausVigo/phangorn
- Documentation: https://pkg.go.dev/github.com/KlausVigo/phangorn#section-documentation
-
Latest release: v2.12.1+incompatible
published over 1 year ago
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced:
10 months ago
proxy.golang.org: github.com/klausvigo/phangorn
- Documentation: https://pkg.go.dev/github.com/klausvigo/phangorn#section-documentation
-
Latest release: v2.12.1+incompatible
published over 1 year ago
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced:
10 months ago
conda-forge.org: r-phangorn
- Homepage: https://github.com/KlausVigo/phangorn
- License: GPL-2.0-or-later
-
Latest release: 2.9.0
published almost 4 years ago
Rankings
Dependent packages count: 8.0%
Dependent repos count: 11.6%
Average: 19.1%
Stargazers count: 27.5%
Forks count: 29.1%
Last synced:
10 months ago
Dependencies
.github/workflows/pkgdown.yaml
actions
- JamesIves/github-pages-deploy-action 4.1.4 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION
cran
- R >= 4.1.0 depends
- ape >= 5.6 depends
- Matrix * imports
- Rcpp * imports
- digest * imports
- fastmatch * imports
- generics * imports
- grDevices * imports
- graphics * imports
- igraph >= 1.0 imports
- methods * imports
- parallel * imports
- quadprog * imports
- stats * imports
- utils * imports
- Biostrings * suggests
- knitr * suggests
- magick * suggests
- rgl * suggests
- rmarkdown * suggests
- seqLogo * suggests
- seqinr * suggests
- tinytest * suggests
- xtable * suggests
.github/workflows/check-standard.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml
actions
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite