package phylogenetics

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Compilation of module signatures used elsewhere.

type index = string

Index type for tree leaves and sequences in alignments

module type BASE = sig ... end

Module type for individual bases (eg, A, T, C, G). Mostly conversion to/from strings and ints

module type SEQUENCE = sig ... end

Module type for sequences of bases (eg, DNA).

module type ALIGNMENT = sig ... end

Module type for alignments of sequences (eg, DNA alignment.)

module type EVOL_MODEL = sig ... end

Evolution model with linear algebra functions to compute static distribution and transition matrix diagonalization.