biopython-sequence-analysis

# Biopython: Sequence Analysis Toolkit ## Overview Biopython provides a comprehensive suite of modules for sequence-centric bioinformatics: reading and writing every major biological file format (FASTA, FASTQ, GenBank, GFF), querying NCBI databases programmatically, running BLAST searches and parsing results, aligning sequences pairwise or in multiple-sequence alignments, and building and visualizing phylogenetic trees. This skill focuses on analysis workflows — from NCBI data retrieval through alignment to phylogenetic inference. For PCR primer design, restriction enzyme digestion, cloning simulation, protein structure analysis (Bio.PDB), and molecular weight/Tm calculations, see **biopython-molecular-biology**. ## When to Use - Download a gene family from NCBI Nucleotide/Protein, align sequences, and construct a phylogenetic tree - Parse GenBank or GFF3 annotation files and extract CDS sequences for a set of features - Run a BLAST search against NCBI `nt` or `nr`, filter significant hits, and fetch their full sequences - Compute pairwise sequence identities or score alignments with BLOSUM62/PAM250 matrices - Index a large multi-FASTA or FASTQ file with `SeqIO.index()` for random-access retrieval without loading all sequences into RAM - Convert between sequence formats (FASTA ↔ GenBank ↔ FASTQ ↔ PHYLIP) in a single call - Traverse, root, prune, and annotate a Newick or Nexus phylogenetic tree programmatically - Use **pysam** instead when working with SAM/BAM/CRAM alignm...