Queer characters, non binary characters, and characters who never even needed to say the word lesbian.
Using simple indel coding added 30 binary characters to the matrix, resulting in 67 variable but parsimony uninformative and 11 parsimony informative characters.
Characters of interest (i.e. state of NA stalk, host type, presence of HA feature and geographic region) were coded as binary characters and estimating the transition rates among the four possible combinations of two binary characters based on phylogenetic trees using the software package BayesTraits [68], [69] (Figure 5).
Hence, our approach was to code binary characters (following [ 28]) and code as neutrally as possible.
Indels were scored in a separate data matrix as binary characters.
Prior to performing phylogenetic analysis, all gaps were coded as binary characters using GapCoder [ 75].
Binary encoding (BE) represents a set of permutations as a matrix of binary characters [ 9].
The MRP matrix is a collection of partial binary characters defined by the input source trees.
The MRP-matrix resembles a multiple sequence alignment with binary characters {0,1} and missing characters.
Gaps (except polyT stretches) were coded as single additional binary characters.
The dataset contained 704 nucleotide characters and eight binary characters, representing indels coded as present (1) or absent (0).
