This repository has been archived

As of September 2025, the scikit-bio team has archived this repository, making it read-only. No further updates to this repository will be made.

The scikit-bio cookbook: delicious and nutritious bioinformatics recipes

This series of Jupyter Notebooks contains executable "recipes" for bioinformatics workflows using scikit-bio.

You can find the table of contents, installation instructions, and other information on the scikit-bio cookbook frontpage.

Name		Name	Last commit message	Last commit date
Latest commit History 187 Commits
assets		assets
data		data
licenses		licenses
skbiocookbook		skbiocookbook
.gitignore		.gitignore
.travis.yml		.travis.yml
Alignment viewing and filtering.ipynb		Alignment viewing and filtering.ipynb
Alignments and phylogenetic reconstruction.ipynb		Alignments and phylogenetic reconstruction.ipynb
COPYING.txt		COPYING.txt
Computing pairwise sequence identity.ipynb		Computing pairwise sequence identity.ipynb
Creating a region-specific reference collection from full-length reference sequences.ipynb		Creating a region-specific reference collection from full-length reference sequences.ipynb
Exploring microbial community diversity.ipynb		Exploring microbial community diversity.ipynb
Finding PCR primers in sequencing products.ipynb		Finding PCR primers in sequencing products.ipynb
Finding the longest stretch of specific characters in a DNA sequence.ipynb		Finding the longest stretch of specific characters in a DNA sequence.ipynb
Index.ipynb		Index.ipynb
Phylogenetic diversity calculations.ipynb		Phylogenetic diversity calculations.ipynb
Progressive multiple sequence alignment.ipynb		Progressive multiple sequence alignment.ipynb
README.md		README.md
Reading and writing files.ipynb		Reading and writing files.ipynb
Six-frame translation of nucleotide sequences.ipynb		Six-frame translation of nucleotide sequences.ipynb
Using the workflow to automate remote database queries.ipynb		Using the workflow to automate remote database queries.ipynb
runipynbs.py		runipynbs.py