Trevor Bedford

Allow halting conditions

5

Each timestep look at genetic diversity, quit simulation if greater than some number.

When extinction occurs, reseed rather restarting. Not clear how to do this best.

Output tree imbalance statistic. Also, decide on which imbalance statistic to use.

Add Tajima's D to output statistics.

Include `colt` random number seed in out.summary.

When there is a coinfection event, there is a certain probability (which could be 100%) at which "recombination" occurs. This mutates the viral phenotypes of both infecting strains. This mutation...

Currently, [each Host references a single virus](https://github.com/trvrb/antigen/blob/master/Host.java#L10). Refactor to have each Host reference an array of viruses, which can be empty. Then, allow new infections to occur at a rate...

I was thinking that a good (easy) way to make things more sharable would be to load the entire `examples/` folder into the drop-down. Here, we'd take out the kruft...

Update download_all to work with segments

2

Current `download_all.py` writes sequences as `h3n2.fasta` etc... However, new augur wants `h3n2_ha.fasta`: https://github.com/nextstrain/augur/tree/master/flu#how-to-run The `download_all.py` script should be updated to download all segments and name them appropriately.

Sort out why Texas/50 is being dropped

1

Some documents are getting dropped in the new upload. The original `tdb` has: ``` A/Stockholm/65/2015 A/Georgia/532/2015 F33/15 NIMR_Feb2016_9_06.csv 160 A/Stockholm/65/2015 A/HongKong/146/2013 F10/15 NIMR_Feb2016_9_06.csv 160 A/Stockholm/65/2015 A/HongKong/4801/2014 F12/15 NIMR_Feb2016_9_06.csv 160 A/Stockholm/65/2015...