Emit IUPAC embiguous nucleotide codes when appropriate
Relaxed and strict clock model files from Rosemary McCloskey
<rmccloskey@cfenet.ubc.ca> in Art Poon's lab.  These files were used in
support of their paper

An Evaluation of Phylogenetic Methods for Reconstructing Transmitted
HIV Variants using Longitudinal Clonal HIV Sequence Data.
Journal of Virology, 88(11), 6181–94.
doi:10.1128/JVI.00483-14

These files have been modified to use Jinja2-style templates from the original beastgen style.
Relaxed and strict clock model files from Rosemary McCloskey
<rmccloskey@cfenet.ubc.ca> in Art Poon's lab.  These files were used in
support of their paper

An Evaluation of Phylogenetic Methods for Reconstructing Transmitted
HIV Variants using Longitudinal Clonal HIV Sequence Data.
Journal of Virology, 88(11), 6181–94.
doi:10.1128/JVI.00483-14

These files have been modified to use Jinja2-style templates from the original beastgen style.
simulate transmission hierarchies in sims/
- add relaxed and strict clock models from McCloskey and Poon
- rewrote templating system to use jinja2
- add python virtual environment for up-to-date version of scipy
- calculate weighted distance from founder sequence for each inferred ancestral sequence