EnvNJ

0.1.3

Whole Genome Phylogenies Using Sequence Environments

0packages depend

2.9Kdownloads / year

81.3%test coverage

0/13checks pass

Overview

About

Maintained by Juan Carlos AledoFirst published 2021-05-312 releasesCRAN page ↗

Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) doi:10.1093/bioinformatics/18.1.100. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)

install.packages("EnvNJ", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-envnj

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-EnvNJ

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 10.8 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 16.77

81.3%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 59%
Documented parameters: 100%
Return-value docs: 100%
References docs: 21%

Downloads

2.9K

CRAN downloads in the past year

Rank #15,901 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

20430 days

71390 days

2.9K1 year

Compare downloads with other packages →

Also on83 r2u

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (7)

ape bio3dgraphicsphangorn philentropy seqinr stringr

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Juan Carlos Aledo

Author, Maintainer

Authors (1)

Juan Carlos Aledo

Author, Maintainer

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.3Latest
2021-09-27 · current release · diff ↗
0.1.2
2021-05-31
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-05-31
Total releases: 2 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 39 KB / 2 files
Download size: 118 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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