Abstract | Introduction | The phylogram package | Importing and exporting trees | Example 1: Import and export a tree from a Newick string | Converting tree objects | Example 2: Convert a "phylo" object to a dendrogram | Tree editing/manipulation | Example 3: Building and manipulating dendrograms | Tree visualization | Summary | Acknowledgements | Author Contributions | References
Package: phylogram 2.1.0.9000
Shaun Wilkinson
phylogram: Dendrograms for Evolutionary Analysis
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
Authors:
phylogram_2.1.0.9000.tar.gz
phylogram_2.1.0.9000.zip(r-4.7)phylogram_2.1.0.9000.zip(r-4.6)phylogram_2.1.0.9000.zip(r-4.5)
phylogram_2.1.0.9000.tgz(r-4.6-any)phylogram_2.1.0.9000.tgz(r-4.5-any)
phylogram_2.1.0.9000.tar.gz(r-4.7-any)phylogram_2.1.0.9000.tar.gz(r-4.6-any)
phylogram_2.1.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phylogram/json (API)
| # Install 'phylogram' in R: |
| install.packages('phylogram', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #212
Bug tracker:https://github.com/ropensci/phylogram/issues
Pkgdown/docs site:https://docs.ropensci.org
Last updated from:9b7ce7672a (on master). Checks:10 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 129 | ||
| pkgdown docs | OK | 154 | ||
| source / vignettes | OK | 175 | ||
| linux-release-x86_64 | OK | 125 | ||
| macos-release-arm64 | OK | 79 | ||
| macos-oldrel-arm64 | OK | 94 | ||
| windows-devel | OK | 70 | ||
| windows-release | OK | 83 | ||
| windows-oldrel | OK | 68 | ||
| wasm-release | OK | 140 |
Exports:as.cladogramas.dendrogramas.dendrogram.phyloas.phyloas.phylo.dendrogramladderpruneread.dendrogramremidpointrepositionwrite.dendrogram
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply unweighted branch lengths. | as.cladogram |
| Convert a "phylo" object to a dendrogram. | as.dendrogram.phylo |
| Convert a dendrogram to a "phylo" object. | as.phylo.dendrogram |
| Reorder tree branches in ladderized pattern. | ladder |
| Dendrograms for evolutionary analysis. | phylogram-package phylogram |
| Remove tree nodes by regular expression pattern matching. | prune |
| Read a dendrogram from parenthetic text. | read.dendrogram |
| Set dendrogram attributes for a nested list. | remidpoint |
| Reset dendrogram height attributes. | reposition |
| Write a dendrogram object to parenthetic text. | write.dendrogram |
