# Biopython Tutorial & Cookbook

Named authors: Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczyński.

This is from Biopython 1.86.

Table of contents:

- Introduction
- Quick Start – What can you do with Biopython?
- Sequence objects
- Sequence annotation objects
- Sequence Input/Output
- Sequence alignments
- Pairwise sequence alignment
- Multiple Sequence Alignment objects
- Pairwise alignments using pairwise2
- BLAST (new)
- BLAST (old)
- BLAST and other sequence search tools
- Accessing NCBI’s Entrez databases
- Swiss-Prot and ExPASy
- Going 3D: The PDB module
- Bio.PopGen: Population genetics
- Phylogenetics with Bio.Phylo
- Sequence motif analysis using Bio.motifs
- Cluster analysis
- Graphics including GenomeDiagram
- KEGG
- Bio.phenotype: analyze phenotypic data
- Cookbook – Cool things to do with it
- The Biopython testing framework
- Where to go from here – contributing to Biopython
- Appendix: Useful stuff about Python
- Bibliography

Biopython v: 1.86

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