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scikit-bio

Python library scikit-bio for biological sequence and community-ecology analysis: DNA/RNA/protein sequences, pair_align alignment, phylogenetic trees (NJ, UPGMA, GME/BME, Newick), alpha/beta diversity including Faith’s PD and UniFrac, PCoA/CCA/RDA ordination, PERMANOVA/ANOSIM/Mantel tests, ancom and dirmult differential abundance, BIOM tables, and FASTA/FASTQ/GenBank I/O. Use when computing microbiome diversity from a BIOM or feature table. Use when running PCoA and PERMANOVA on a distance matrix. Use when building or comparing phylogenetic trees from sequences. Use when reading, converting, or aligning FASTA/FASTQ/GenBank/Newick data. Use when testing differential abundance in compositional count data. Not for general-purpose sequence scripting where Biopython is enough.

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Install

npx research-agent-skills install scikit-bio
npx skills add KalarisLabs/research-agent-skills --skill scikit-bio

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When to use it

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Full playbook