aphid

1.3.6

Analysis with Profile Hidden Markov Models

2packages depend

8.7Kdownloads / year

63.6%test coverage

11/13checks pass

Overview

About

Maintained by Shaun WilkinsonFirst published 2017-06-2410 releasesCRAN page ↗GitHub ↗

Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("shaunpwilkinson/aphid")

Development version from shaunpwilkinson/aphid. Installs pak first if it is not already available.

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-aphid

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-aphid

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

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

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-aphid

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 3.6 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.04

63.6%

Coverage · measured lines

Dependencies · direct

Check history

NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 295 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 73%

Downloads

8.7K

CRAN downloads in the past year

Rank #6,160 · ~24/day · ~724/mo

Releases R versions

Daily download trend is not available in this view yet.

51230 days

1.5K90 days

8.7K1 year

Compare downloads with other packages →

Also on485 r2u44 autocran1.3K conda_forge116 c2d4u

Repository

GitHub ↗ shaunpwilkinson/aphid

22Stars

4Forks

10Open issues

1Open PRs

2Releases

223Commits

2Contributors

223 commits · Last activity 2026-01-23

Stars over time

2024-10-15 · 222026-07-07 · 22

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/shaunpwilkinson/aphid on 2026-07-26.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (6)

graphicsopenssl kmer qpdf Rcppstats

LinkingTo (1)

Rcpp

Suggests (4)

ape knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

1indirect

debar insect

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Shaun Wilkinson

Author, Maintainer

Authors (1)

Shaun Wilkinson

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.6Latest
2026-01-23 · current release · diff ↗
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
1.3.5
2022-12-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.3.3
2019-05-08 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.3.2
2019-03-15 · diff ↗
1.3.1
2018-11-10 · diff ↗
1.3.0
2018-10-09 · diff ↗
1.2.0
2018-08-14 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 4 earlier events

1.1.0
2018-03-16 · diff ↗
1.0.1
2017-07-07 · diff ↗
1.0.0
2017-06-24
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-06-24
Total releases: 10 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 27 KB / 3 files
Download size: 261 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Report a problem with this page →