The FuturePhy folks have funds for (among other things) a series of hackathons. Given that focused events seem more productive than general “hacking on phylogenetics” events, what topics in phylogenetics could use a hackathon to move things forward?
I think a session focused on data filtering for phylogenetics would be really good. There is a lot of conversation about ‘more data vs. better models’, but not quite as much conversation about using data that work with our models. Coding up some tests for model violations and other methods for data filtering could be particularly useful. @rob_lanfear and I have spoken a lot about this and I think it could be a good fit for a collaborative environment like a hackathon.
Please join us for the first FuturePhy webinar on June 11 at 2P ET, where some of the organizers will summarize the aims of the project and outline the opportunities for community participation. We are using an Adobe Connect meeting room at https://distance-pilot.uchicago.edu/mwestneat/
My vote is to have a lot of attention devoted to site-heterogeneity in phylogenetic modeling. Specifically, fast approximate methods for evaluating mixture models that account for different site ‘types’. To my mind this is THE most important improvement in phylogenetic modeling w.r.t. model realism and it is also computationally demanding for very large data sets (i.e. large in terms of both numbers of sites in super-matrices and numbers of taxa).
Have you seen this: https://github.com/HullUni-bioinformatics/ReproPhylo ?
Jupyter-based phylogenetics (Jupyter = replacement for ipython notebooks). I think this is a great step in the right direction, but needs integration with other tools / methods.