Package: maxaltall
Type: Package
Title: 'FASTA' ML and ‘altall’ Sequences from IQ-TREE .state Files
Version: 0.1.0
Authors@R: c(person(given = c("Alec", "S."),
                      family = "Chu",
                      role = "aut"),
               person(given = c("Philip", "D."),
                      family = "Kiser",
                      role = c("aut", "cre"),
                      email = "pkiser@uci.edu"))
Maintainer: Philip D. Kiser <pkiser@uci.edu>
Description: 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>.
License: GPL (>= 3)
Imports: data.table, dplyr, magrittr, tidyr
Encoding: UTF-8
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2026-10-04 08:10:54 UTC; root
Author: Alec S. Chu [aut], Philip D. Kiser [aut, cre]
Config/pak/sysreqs: libicu-dev
Repository: https://pdkiser.r-universe.dev
Date/Publication: 2024-09-25 09:30:02 UTC
RemoteUrl: https://github.com/cran/maxaltall
RemoteRef: HEAD
RemoteSha: 8fabedea45b1dce2ecc44ef26beff87303cbc6d6