implementation of generalized Robinson-Foulds metric for comparing trees
- LEMON 1.3
- ILOG CPLEX (>= 12.0)
Get yoshiko from github:
git clone <HTTPS clone URL (see on the right side of this page)>
First, LEMON 1.3 needs to be installed:
wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.tar.gz
tar xvzf lemon-1.3.tar.gz
cd lemon-1.3
cmake -DCMAKE_INSTALL_PREFIX=~/lemon
make install
Note: On Mac OS 10.9, comment out the following two lines and add the code below at line 162 in CMakeLists.txt before make install
#ADD_SUBDIRECTORY(demo)
#ADD_SUBDIRECTORY(tools)
if( ${CMAKE_SYSTEM_NAME} MATCHES "Darwin" )
set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++ " )
endif()
You can remove the LEMON sources now, i.e., rm -rf lemon-1.3.
CPLEX is a commercial product owned by IBM. For academic purposed it can be obtained at no charge via IBM's Academic Initiative programme:
http://www-03.ibm.com/ibm/university/academic/pub/page/membership
Next, JRF can be compiled:
mkdir build
cd build
cmake ..
make
In case auto-detection of LEMON or CPLEX fails, do
cmake \
-DLIBLEMON_ROOT=~/lemon \
-DCPLEX_INC_DIR=~/ILOG/cplex/include/ \
-DCPLEX_LIB_DIR=~/ILOG/cplex/lib/x86-64_osx/static_pic \
-DCONCERT_LIB_DIR=~/ILOG/concert/lib/x86-64_osx/static_pic \
-DCONCERT_INC_DIR=~/ILOG/concert/include/ ..
To run JRF on two small toy trees:
./JRF -t1 ../data/t1.txt -t2 ../data/t2.txt -v 4
This will create output similar to
../data/t1.txt|../data/t2.txt 1 16 0 0 3.99127 7 0 4.65794 4.65794 0 7 0
The numbers have the following meaning (in order of occurence):
1: value of k
16: Robinson-Foulds distance (RF)
0: #internal nodes in t1 + #internal nodes in t2 -RF
0: time to compute RF
3.99127: cost of minimum cost bipartite matching (MCBM)
7: number of conflicts induced by MCBM
0: time to compute MCBM
4.65794: lower bound on minimum cost arboreal bipartite matching (MCABM)
4.65794: upper bound on MCABM
0: optimality gap
7: number of clade pairs matched by MCABM
0: time to compute MCABM
Get a list of options:
./JRF -h