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README.md

PuReD-MCL

clustering of related PubMed documents


server: http://bat.infspire.org/tools/pured-mcl
citation: http://www.ncbi.nlm.nih.gov/pubmed/18593717
code: we provide the main Perl script, and the server's CGI script and HTML page - you'll need MCL and few Perl modules
usage:
before you run PuReD-MCL, be sure to:
- have Stijn van Dongen's MCL installed and in your path
- have installed the following Perl modules:
	Getopt::Long
	LWP::Simple
	XML::LibXML::Reader

pured-mcl.pl

either --query query you want to perform in PubMed, enclose it in double quotes or --xml results from PubMed in XML format

other (optional) arguments --min define the minimum inflation for MCL (smaller the value, larger/fewer the clusters) [default=2.0] --max define the maximum inflation for MCL (larger the value, smaller/more the clusters) [default=2.0] --step define the increment step to reach the maximun inflation from the minimum [default=1.0] --max_doc define the maximum number of documents you want to handle [default=10,000]

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clustering of related PubMed documents

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