baltic: the Backronymed Adaptable Lightweight Tree vIsualisation Code

For over a decade, the open-source Python library known as baltic has served as a powerful tool in the visualization of annotated phylogeny figures across various fields, including molecular epidemiology. This has been crucial during notable events such as the West African Ebola epidemic, the Zika virus outbreak in the Americas, and the global COVID-19 pandemic.

At the heart of baltic is a compact library designed for the efficient parsing, traversal, manipulation, and visualization of phylogenetic trees. With minimal dependencies, it is adept at handling common tree formats utilized in phylodynamic analyses. Its primary function is to empower users to interact with a lightweight tree data structure, enabling them to generate publication-ready figures using matplotlib.

In a significant update, baltic v1.0 has been officially released, featuring a host of new capabilities. It can now read and write files in BEAST Nexus, Newick, and Nextstrain/Auspice JSON formats. This version is capable of processing substantial BEAST posterior tree files in parallel, extracting user-defined posterior statistics from them.

One of the most notable enhancements is the inclusion of several rooting methods, such as midpoint rooting, rerooting on any branch, and root-to-tip regression. Furthermore, it has expanded its support to accommodate reticulate evolution, allowing for the representation of reassortment and recombination events through edges in the tree.

Additionally, baltic v1.0 introduces the functionality to create composite figures that merge phylogenetic trees with other data types. This includes Muller plots, skygrid plots, tanglegrams, and plots that connect trees to geographical maps. The release also comes with a comprehensive documentation site, featuring an API reference, tutorials, and a gallery of matplotlib-style examples, providing users with a wealth of resources for effectively utilizing the library's capabilities.