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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 gmail.com if you would like to help modify the code.

Deprecated

There is another BioPHP that is much better than this one, labeled as Mark's biophp on http://biophp.org.

About

This is Lee Katz's set of PHP classes for bioinformatics. This is not related at all to the biophp.org 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

Installation

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

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

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