diff --git a/Makefile.config b/Makefile.config
index c589af5..b857739 100644
--- a/Makefile.config
+++ b/Makefile.config
@@ -1,18 +1,19 @@
 # C++ compiler
 CCC = g++
+
 # Compiler flags (you probably don't need to change anything here)
 CCCFLAGS = -O2 -m64 -std=gnu++0x -Wall
-# include directory
-CCCINC = -I../Common/ -I/usr/include/bamtools
-# library directory and libraries
-CCCLIB = -lbamtools
+
+# Include directories
+CCCINC = -I../Common/ -I/usr/include/bamtools -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include -I/data/bio/alexeygritsenk/apps/ILOG/concert/include -I/usr/include/ncbi-tools++
+
+# Library directories and libraries
+CCCLIB = -lbamtools -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert -lm -pthread
 
 # Extra flags. Used for compiling scaffoldOptimizer (it uses the NCBI C++ Toolkit and CPLEX API)
 CCEFLAGS = -fPIC -fexceptions -fopenmp -DNDEBUG -DIL_STD
-CCEINC = -I/data/bio/alexeygritsenk/apps/ILOG/cplex/include -I/data/bio/alexeygritsenk/apps/ILOG/concert/include -I/usr/include/ncbi-tools++
-CCELIB = -lxalgoalignnw -lxobjmgr -lgenome_collection -lseqset -lseqedit -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -ltables -L/data/bio/alexeygritsenk/apps/ILOG/cplex/lib/x86-64_sles10_4.1/static_pic -lilocplex -lcplex -L/data/bio/alexeygritsenk/apps/ILOG/concert/lib/x86-64_sles10_4.1/static_pic -lconcert -lm -pthread
 
-# Do not change anything below unless (you think) you know what you're doing.
+# Do not change anything below unless you are familiar with it.
 MAKE = make
 MD = mkdir
 CDIR = ../Common