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Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics.

All code, images and documents in this repository are freely available for all uses. Code is available under the MIT license and images, documentations and talks under the Creative Commons No Rights Reserved (CC0) license.

Some projects which may be especially interesting:

  • CloudBioLinux -- An automated environment to install useful biological software and libraries. This is used to bootstrap blank machines, such as those you'd find on Cloud providers like Amazon, to ready to go analysis workstations. See the CloudBioLinux effort for more details. This project moved to its own repository at
  • gff -- A GFF parsing library in Python, aimed for inclusion into Biopython.
  • nextgen -- A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. This project has moved into its own repository:
  • distblast -- A distributed BLAST analysis running for identifying best hits in a wide variety of organisms for downstream phylogenetic analyses. The code is generalized to run on local multi-processor and distributed Hadoop clusters.