Muller

- Improved the speed of the scripts ~40% on large datasets.
- Added a `--no-outlines` option to disable the white outlines in the muller plots.

- Implemented a scoring system for detecting genotype lineage.
- Modified the colorscheme to highlight significant nodes when there are a large number of genotypes.
- Changed the available options controlling the nesting step.
- Adjusted the genotype clustering algorithm to account for genotypes that fix immediately.
- Changed how the lineage plots were implemented. They now use pygraphviz (rather than the mermaid language) and are now annotated with the mutations each genotype represents.
- Updated a large amount of the documentation. The markdown version was split into separate files. The latex version is a work in progress.
- Changed the example dataset to highlight the annotation feature.
- Fixed a large number of bugs.

This is the first release of this package. It was used on a set of three mouse populations involved in an evolutionary dynamics experiment. The `user_manual.md` file in the `docs` folder explains in detail the math and rationale behind the scripts.