phyca: phylogeny and collinearity aware assembly evaluation toolkit
phyca is built around Compleasm utilizing the NCBI Genome database. For a query assembly, phyca improves the precision of BUSCO/Compleasm annotations by up to 7%, makes syntenic comparisons to public reference genomes and rapidly places the assembly on a broad, precomputed phylogeny.
Source and documentation: https://github.com/DeadlineWasYesterday/phyca/
BioNick: Software for manipulating newick strings and adding phylogenies to Matplotlib visuals
BioNick includes a series of modular functions for the manipulation of Newick strings in python, e.g., extracting leaves, swapping roots, removing node labels, flipping the order of nodes, removing leaves, extracting subtrees, visualizing cladograms with matplotlib visuals, etc. BioNick is also equipped with the ability to represent trees as a collection of node objects and create Neighbor-Joining trees from distance matrices.
Source and documentation: https://github.com/DeadlineWasYesterday/BioNick/