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biopython-alignment

separate

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.

When to use

• You need **global alignment** between two protein (or nucleotide) sequences and want a reproducible score and aligned strings.
• You need **local alignment** to find the best matching fragment/subsequence between two DNA/RNA/protein sequences.
• You need to **read, write, or convert** multiple sequence alignment (MSA) files (e.g., FASTA/Clustal/Stockholm) using Biopython I/O.
• You want to compute **alignment statistics** (e.g., identity, coverage, conservation per column) and filter alignments by thresholds.
• You need to apply **substitution matrices** (e.g., BLOSUM62) and tune gap penalties for biologically meaningful scoring.

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