Approximate subgraph isomorphisms for biological networks
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Alignment.cpp
Alignment.h
Archive.cpp
Archive.h
LICENSE.txt
Makefile
Network.cpp
Network.h
README.md
argParsing.h
blastinfo.cpp
blastinfo.h
example.sim
example1.annos
example1.net
example2.annos
example2.net
generateExperiments.py
generateExperimentsSteadyState.py
goc.cpp
goc.h
hillclimber.cpp
localSearch.cpp stack allocate old fitness for reduction of runtime by 1/9. Use corre… Jul 11, 2014
localSearch.h
manual.tex
nsga-ii.cpp
nsga-ii.h
nsgaiimain.cpp
steadystate.cpp switch from tbb atomics to C++11 atomics Feb 6, 2016
tests.cpp
threadTest.cpp fixed bug where crowding distance wasn't being computed for last front May 30, 2014
timetest.sh store GOC and bitscore data in multi_array for performance increase Jul 10, 2014
todo.txt

README.md

optnetaligncpp

Optimizing network aligner

Quick start

Install the C++ Boost libraries on your system, then do the following:

make optnetalignubuntu
./optnetalign --net1 scere.net --net2 dmela.net --total --s3 --bitscores sc-dm.sim --blastsum --annotations1 scere.annos --annotations2 dmela.annos --cxrate 0.05 --cxswappb 0.75 --mutrate 0.05 --mutswappb 0.0001 --oneobjrate 0.75 --dynparams --popsize 200 --generations 1000000000 --hillclimbiters 10000  --timelimit 720 --outprefix sc-dm1 --finalstats >> sc-dm1.finalstats

For more information, see manual.tex