v1.0.0

• Setting version to 1.0.0 since it's not pre-release anymore.
• Updated README with info on environment setup and usage.
• Updated vignette with detailed instructions on environment setup.
• Changed file extension for printing trees to .pdf with argument to specify what is wanted.
• Added some code to identify which variants are most variant across specified populations of cells. I also put in code to call variants at just these locations across individual cells to speed up the process. Just a word of warning, this is still fairly slow and most of your cells will lack calls at many of these positions due to low coverage.