scikit-bio

Sequence alignment in scikit-bio supports pairwise and multiple alignments for DNA, RNA, and protein sequences. Load sequences from FASTA/FASTQ files, apply alignment algorithms, and retrieve scored alignments to identify similarities and differences across your biological data.

Yes, scikit-bio provides file I/O for FASTA, FASTQ, GenBank, Newick, and BIOM formats. Stream large datasets efficiently, parse sequences with metadata, and export results back to standard bioinformatics formats without manual format conversion.

Construct phylogenetic trees from sequence alignments using distance metrics and tree-building methods. scikit-bio handles tree construction, manipulation, and traversal, enabling phylogenetic inference and evolutionary analysis for DNA, RNA, or protein sequences.

Alpha and beta diversity metrics quantify species richness and community differences in microbiome studies. scikit-bio calculates these metrics, performs ordination like PCoA, and supports UniFrac analysis to compare microbial communities across samples.

Scikit-bio handles DNA/RNA/protein manipulation including reverse complement, translation, and motif search. Combine these operations in batch processing workflows to extract biological features and prepare sequences for downstream alignment or phylogenetic analysis.

Scikit-bio integrates diversity metrics, ordination (PCoA), and statistical tests like PERMANOVA in one toolkit. Process microbiome or ecological data end-to-end: compute alpha/beta diversity, perform ordination, and test significance without switching between multiple libraries.