Source: https://github.com/aipoch/medical-research-skills

When to Use

You need to parse, validate, and manipulate biological sequences (DNA/RNA/protein) and their metadata.
You are running microbiome/community-ecology workflows (alpha/beta diversity, UniFrac, ordination, PERMANOVA).
You need to build, transform, or compare phylogenetic trees (Newick I/O, pruning/rerooting, patristic distances).
You want to compute and work with distance matrices and downstream multivariate analyses (PCoA, Mantel, ANOSIM).
You need to read/write common bioinformatics formats (FASTA/FASTQ, Newick, BIOM) and convert between them.

Key Features

Sequence objects: DNA, RNA, Protein, and generic Sequence with validation, slicing, motif search, reverse complement, transcription/translation, and metadata handling.
Alignment utilities: pairwise local alignment (SSW-based) and multiple sequence alignment containers (TabularMSA) with consensus support.
Phylogenetics: TreeNode manipulation, tree construction from distance matrices (e.g., Neighbor Joining), and tree distance/metrics.
Diversity: alpha diversity (e.g., Shannon, Faith’s PD) and beta diversity (e.g., Bray-Curtis, UniFrac) returning Series/DistanceMatrix.
Ordination & stats: PCoA and ecological hypothesis tests (PERMANOVA, ANOSIM, Mantel) operating on distance matrices.
I/O ecosystem: FASTA/FASTQ and Newick reading/writing; BIOM table support via Table.