checkpoint analysis doc before embarking on an interactive exploration
corrected transmission structure

- modify mksanat to work on fasta files with unstructured names.  now we can use a consistent procedure to create the first config from raw hiv-pol fasta file.
- change mkbeast to simply use generation numbers as days when associating dates with taxons
- add hiv-pol as outgroup.  Probably want to do this from mkbeats instead of through the templates for more flexibility.