maxaltall

0.1.0

'FASTA' ML and ‘altall’ Sequences from IQ-TREE .state Files

0packages depend

6.8Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Philip D. KiserFirst published 2024-09-251 releasesCRAN page ↗

Takes a .state file generated by IQ-TREE as an input and, for each ancestral node present in the file, generates a FASTA-formatted maximum likelihood (ML) sequence as well as an ‘AltAll’ sequence in which uncertain sites, determined by the two parameters thres_1 and thres_2, have the maximum likelihood state swapped with the next most likely state as described in Geeta N. Eick, Jamie T. Bridgham, Douglas P. Anderson, Michael J. Harms, and Joseph W. Thornton (2017), "Robustness of Reconstructed Ancestral Protein Functions to Statistical Uncertainty" doi:10.1093/molbev/msw223.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("maxaltall", 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-maxaltall

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

# 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-maxaltall

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

Health

CRAN checks

13OK

Slowest check: 1.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

6.8K

CRAN downloads in the past year

Rank #7,313 · ~19/day · ~570/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

1.4K90 days

6.8K1 year

Compare downloads with other packages →

Also on100 r2u31 autocran

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

data.table dplyr magrittr tidyr

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Philip D. Kiser

Author, Maintainer

Authors (2)

Philip D. Kiser

Author, Maintainer

Alec S. Chu

Author

Listed in earlier versions (2)

Chu

no longer listed · 0.1.0

Kiser

no longer listed · 0.1.0

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-09-25
Total releases: 1 / 2 yrs
License: GPL (>= 3) OSI
Download size: 167 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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