The following functions organize information that gets passed to
to generate variants from a reference genome.
Each function represents a method of generation and starts with
The first three are phylogenomic methods, and all functions but
will use molecular evolution information when passed to
Uses an estimate for theta, the population-scaled mutation rate, and a desired number of variants.
Uses phylogenetic tree(s) from
object(s) or NEWICK file(s), one tree per sequence or one for all sequences.
Uses gene trees, either in the form of
an object from the
coala package or
a file containing output in the style of the
Uses matrices of segregating sites,
either in the form of
coala coalescent-simulator object(s), or
ms-style output file.
Uses a variant call format (VCF) file that
directly specifies variants.
This method does not work if the
vcfR package isn't installed.