Package: maxaltall 0.1.0

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

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>.

Authors:Alec S. Chu [aut], Philip D. Kiser [aut, cre]

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maxaltall.pdf |maxaltall.html✨
maxaltall/json (API)

# Install 'maxaltall' in R:
install.packages('maxaltall', repos = c('https://pdkiser.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 535 downloads 1 exports 22 dependencies

Last updated 2 months agofrom:8fabedea45. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winOKOct 27 2024
R-4.5-linuxOKOct 27 2024
R-4.4-winOKOct 27 2024
R-4.4-macOKOct 27 2024
R-4.3-winOKOct 27 2024
R-4.3-macOKOct 27 2024

Exports:max_altall

Dependencies:clicpp11data.tabledplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr