Biopython

Biopython is the long-standing general-purpose library for computational biology in Python — sequence handling, file parsing, database access and structural work. It is unglamorous, it has been maintained for over two decades, and it is in the dependency tree of a large share of bioinformatics software.

What it does

Its most-used capability is parsing: FASTA, FASTQ, GenBank, PDB, BLAST output and dozens of other formats, handled correctly including the edge cases that break hand-written parsers. Beyond that it covers sequence manipulation, alignment interfaces, NCBI Entrez access, phylogenetics and PDB structure handling.

Strengths

• Free and open source, with two decades of maintenance behind it.
• Correct parsers for a very large set of formats.
• Sensible programmatic access to NCBI databases.
• Stable API that does not break between releases.
• Extensive documentation and an enormous body of example code.

Limitations

It is a general toolkit, so specialised tasks are better served by focused libraries — pysam for alignment files, scikit-bio for some analyses. Parts of the API show their age, and performance on very large files is unremarkable next to compiled tools. It is a building block for writing analyses, not an analysis you can run.