My favorites | Sign in
Project Home Downloads Wiki Issues Source
Project Information

Introduction to biophp project

I'm not too savvy on wikis or group projects, but I think this is something that we can all work on. Please contact me at lskatz+biophp at if you would like to help modify the code.


There is another BioPHP that is much better than this one, labeled as Mark's biophp on


This is Lee Katz's set of PHP classes for bioinformatics. This is not related at all to the project. Lee Katz is a PhD student at The Georgia Institute of Technology, in Atlanta, GA, USA.

Functions so far include

  • read/write fasta files
  • read/write alignment files
  • wrappers for
    • BLAST (and other NCBI tools)
    • Clustal
    • Muscle


To install, unpack all files into a biophp directory. At the beginning of any php file that you want to use biophp with,

<? require_once "biophp/Bio.php"; ?>


Documentation is still lacking, but each file is heavily commented.

Powered by Google Project Hosting