scikit-bio

scikit-bio is an agent skill for biological data work with the scikit-bio Python toolkit, targeting version 0.7.4. It covers sequence manipulation and alignment, phylogenetics, microbial ecology and multivariate statistics. Use it to read and write biological file formats such as FASTA, FASTQ, GenBank, Newick and BIOM, to search for motifs, to build and analyse phylogenetic trees, and to calculate diversity measures. Those measures include alpha and beta diversity and UniFrac distances. It also covers ordination such as PCoA, CCA and RDA, and statistical tests for community data, including PERMANOVA, ANOSIM and the Mantel test. Microbiome and community ecology work fits here, as does handling protein embeddings from language models. The native tests use small synthetic fixtures, and examples that name files or leave inputs undefined are workflow templates to adapt. A review file records the evidence and the boundaries. Use it for ecology, microbiome or sequence analysis in Python. It is part of the k-dense-ai scientific agent skills repository on GitHub, which has about 49,600 stars. The listing shows it as free, and it has about 1,800 installs.…