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REQUIREMENTS:
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The SAVAGE program is a combination of C++ code (which has to be compiled) 
and Python scripts (version 2.6 or later, but not Python 3.x). The C++ part
requires several boost libraries (boost::timer, boost::system, and 
boost::program_options) and it needs OpenMP.

SAVAGE uses the quick-cliques package 
(https://github.com/darrenstrash/quick-cliques) for maximal clique 
enumeration. It needs the cliques to be output one-by-one, as is the case in 
the included quick-cliques release.

Similarly, SAVAGE uses the SFO package 
(https://www.cs.helsinki.fi/group/suds/sfo/) for computing all approximate 
suffix-prefix overlaps (de novo mode). This package is also included.

Finally, SAVAGE requires 'makeblastdb' and 'blastn' from the ncbi toolkit. 
Follow the installation instructions on 
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/


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INSTALLATION:
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Download the git repository and change to the extracted directory, then use 
make:

$ git clone https://jbaaijens@bitbucket.org/jbaaijens/savage.git
$ cd savage
$ make
