Full package name: mesquite.distance.F81Distance.F81Distance Duty: (mesquite.distance.lib.TaxaDistFromMatrix)
Module Explanation
F81 (Felsenstein, 1981) distance from a character matrix.
Author(s): Wayne P. Maddison and David R. Maddison
Version 3.70
Commands of F81 distance
toggleBaseFreqEntireMatrix
Explanation: Sets whether the base frequency values used in distance calculations are based upon the entire matrix (if on) or just the pair of sequences being compared (if off).
Parameters: [on; off]
toggleCountDifferencesIfGapInPair
Explanation: Sets whether sites at which one element of the pair of sequences being compared has a gap are not excluded or are.
Parameters: [on; off]
toggleEstimateAmbiguityDifferences
Explanation: Sets whether sites with missing data, gaps, or ambiguities have differences estimated by other sites or are ignored.
