I made these changes starting from your master branch, so the merge shouldn't be too difficult. Still you'll probably want to pull it into a new branch first before pulling into your master.
I changed the names of some functions, cleaned up the code a lot, implemented a persistent Popen object for calling seq-gen (big speed improvement) and changed the height rescaling when passing trees to seq-gen (I think it is right now in giving exp. subst./site). I also made modified the functions for writing data to phylip (you could easily add fasta support back in), and optimized the raxml inference tool (you could easily mod iqtree back in).
Hey Patrick,
I pushed a ton of updates to ipcoal this weekend, and put together some starting docs (https://ipcoal.readthedocs.io/en/latest/index.html). These are all on the eaton-lab fork currently.
I made these changes starting from your master branch, so the merge shouldn't be too difficult. Still you'll probably want to pull it into a new branch first before pulling into your master.
I changed the names of some functions, cleaned up the code a lot, implemented a persistent Popen object for calling seq-gen (big speed improvement) and changed the height rescaling when passing trees to seq-gen (I think it is right now in giving exp. subst./site). I also made modified the functions for writing data to phylip (you could easily add fasta support back in), and optimized the raxml inference tool (you could easily mod iqtree back in).
You'll need to pull in the latest toytree.
Best, Deren