NEXCISION

Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the [Open Bioinformatics Foundation](http://open-bio.org/). Contains the very useful [Entrez](https://biopython.org/DIST/docs/api/Bio.Entrez-module.html) package for API access to the NCBI databases.

BRANCHSNV reports strict clade-exclusive nucleotide markers separately from single-nucleotide substitutions reconstructed on a selected edge of a rooted phylogenetic tree, while retaining ambiguity across equally parsimonious ancestral-state reconstructions.

Scalable genomic analysis.

Pythonic access to FASTA files.

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

Phylo-Movies is an open-source React and Flask web application, also available as a desktop app, for inspecting ordered phylogenetic tree series. It computes and visualizes subtree-prune-and-regraft transition frames between consecutive trees, helping users see which taxa or subtrees move across sliding-window analyses, bootstrap replicates, and curated tree-series comparisons. The viewer includes timeline playback, tree comparison, MSA context, coloring, analytics, image export, and recording tools.