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>.