# jackalope 1.1.0

- Fixed bug when scaling tree using theta parameter.
- Using “haplotypes” instead of “variants” throughout.
- Updated
`R6`

class documentation for new `roxygen2`

methods.
- Provide method to merge >1 chromosomes, but not the whole genome

# jackalope 1.0.0

`create_variants`

performs better with high mutation rates
- Substitutions now use a random-site, discrete-Gamma model for among-site variability (optionally with invariant sites), rather than a fixed-sites model
- No longer depends on
`vcfR`

package, instead using `htslib`

for reading VCF files
- Indel creation now uses “tau-leaping” approximation to the Doob-Gillespie algorithm
- Substitutions are added by calculating transition-probability matrices and sampling for substitutions at each site