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

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>.

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