- Read, manipulate and write .jplace files
- Extract, filter and merge placements
- Calculate distance measures (e.g., Earth Movers Distance)
- Visualize read abundances on the branches of the tree
Could you describe the differences from our
guppy, which does all of those things?
The main difference is that genesis is a library, for both C++ and Python. This makes it flexible and offers different use cases:
In addition, the currently available functions are different ones than the ones guppy offers. I did not want to create a copy/replacement for guppy but instead offer new complementary methods. For example:
There are also some helpful out-of-the-box tools to be used. Currently, there are two demo programs (http://doc.genesis-lib.org/demos.html) for visualizing placements and for extracting them from clades of the tree. I will add more in the future.
As a final remark, I am open to feature requests. Maybe it’s just a three-liner, and it is always good to get a feeling about what kind of functionality is needed by the community.
That’s cool, @lczech! Thanks for the update. I should also say that in general it’s a good thing for there to be at least two software packages doing the same thing.
I’m not sure if I quite understand. Guppy’s KR can move about mass from individual placements, split by their likelihood weight ratio or posterior probability.