* Removed seaborn as a dependency in favor of base matplotlib ([13][]) * Set default learning rate for t-SNE to "auto" such that the learning rate scales with the sample size ([12][])
Features
* Add support for multiple alignment and/or distance matrix inputs to `pathogen-embed` ([19][]) * Add optional output from `pathogen-embed` that produces the boxplot figure of Euclidean by genetic distance ([14][])
Bug Fixes
* Display default parameters for subcommands of pathogen-embed ([12][])
* Fix t-SNE keyword argument error associated with recent versions of scikit-learn ([6][]) * Pass random seed argument from the command line to PCA and MDS implementations ([6][])
Features * Add stress value dataframe to MDS arguments to relay fitness of the embedding
1.0.0
Major Changes
* Created separate commands for embedding, clustering, and distance matrix creation (pathogen-embed, pathogen-cluster, pathogen-distance) ([2](https://github.com/blab/pathogen-embed/pull/2))