EDIT (03/18/2021): Now published in mSystems! See the paper here!
Excited to announce that the pre-print of our newest work on EMPress is out in bioRxiv today! EMPress is an interactive phylogenetic tree viewer that helps researchers explore the relationships among hierarchically organized features. For example, if you have an insertion tree of 16S sequences and sample and/or feature metadata you can use EMPress to inform your future analyses!
EMPress is a great tool because it streamlines a process that was often cumbersome beforehand. For example, the Interactive Tree of Life (iTOL) visualizer required users to upload individual files for each metadata category. This was fairly tedious for me and I often ran into issues formatting the files correctly. In EMPress, this process is much more intuitive. Feature metadata can be displayed as either colored tips or a layer of tip-aligned barplots. If you are interested in which features are specific to certain sample metadata categories, you can color tips by sample metadata as well! EMPress also allows users to search for nodes of interest through textual searching in case you have a particular interest in a specific feature.
Another great feature of EMPress is its ability to visualize trees with many nodes. We ran EMPress on a tree of the EMP data that ended up being over 300,000 tips and over 26,000 samples! EMPress also has the option of viewing the interactive tree in tandem with an EMPeror plot of samples. Selecting samples in the ordination will show the corresponding features in the tree. This functionality also works in the opposite direction if the ordination is a biplot: selecting an arrow in the EMPeror plot will highlight it in EMPress!
I helped out with some of the code and unit testing as well as generating the visualizations for Figure 1. A Jupyter Notebook describing the generation of these visualizations can be found here.
There’s a ton you can do with EMPress and more on the way! Check out the preprint here and we hope you consider using EMPress for your phylogenetic analyses in the future!