# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "maxaltall" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'maxaltall: ''FASTA'' ML and ‘altall’ Sequences from IQ-TREE .state Files'
version: 0.1.0
doi: 10.32614/CRAN.package.maxaltall
abstract: 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" <https://doi.org/10.1093/molbev/msw223>.
authors:
- family-names: Chu
  given-names: Alec S.
- family-names: Kiser
  given-names: Philip D.
  email: pkiser@uci.edu
repository: https://pdkiser.r-universe.dev
commit: 8fabedea45b1dce2ecc44ef26beff87303cbc6d6
date-released: '2024-09-25'
contact:
- family-names: Kiser
  given-names: Philip D.
  email: pkiser@uci.edu