diff --git a/Makefile b/Makefile
deleted file mode 100644
index 6d0a141..0000000
--- a/Makefile
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright (C) 2018-2019 Andrew D. Smith
-#
-# Authors: Andrew D. Smith
-#
-# This file is part of ABISMAL.
-#
-# ABISMAL is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# ABISMAL is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
-# License for more details.
-#
-SMITHLAB_CPP=$(abspath $(dir $(MAKEFILE_LIST)))/src/smithlab_cpp
-SRC_ROOT=$(shell pwd)
-
-	ifeq (,$(wildcard $(SMITHLAB_CPP)/Makefile))
-	$(error src/smithlab_cpp does not have a Makefile. \
-					Did you use --recursive when running git clone?)
-	endif
-
-all:
-	@$(MAKE) -C $(SMITHLAB_CPP) all
-	@$(MAKE) -C src SRC_ROOT=$(SRC_ROOT) OPT=1 all
-
-libabismal.a:
-	@$(MAKE) -C src SRC_ROOT=$(SRC_ROOT) libabismal.a
-
-install:
-	@$(MAKE) -C src SRC_ROOT=$(SRC_ROOT) OPT=1 install
-
-clean:
-	@$(MAKE) -C $(SMITHLAB_CPP) clean
-	@$(MAKE) -C src clean
-	@-rm -f *.o *.a *~
-.PHONY: clean
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index 9ef7485..0000000
--- a/src/Makefile
+++ /dev/null
@@ -1,75 +0,0 @@
-# Copyright (C) 2018-2019 Andrew D. Smith
-#
-# Authors: Andrew D. Smith
-#
-# This file is part of ABISMAL.
-#
-# ABISMAL is free software: you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# ABISMAL is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
-# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
-# License for more details.
-
-# check if recursive clone was done
-SMITHLAB_CPP = $(abspath $(dir $(MAKEFILE_LIST)))/smithlab_cpp
-STATIC_LIB = $(addprefix $(SRC_ROOT)/, libabismal.a)
-
-BINARIES = abismal abismalidx simreads
-OBJECTS = abismal.o abismalidx.o simreads.o AbismalIndex.o
-
-ifeq (,$(wildcard $(SMITHLAB_CPP)/Makefile))
-$(error src/smithlab_cpp does not have a Makefile. \
-	Did you use --recursive when running git clone?)
-endif
-
-PROGS = $(BINARIES)
-CXX = g++
-CXXFLAGS = -Wall -std=c++11
-LDLIBS = -lz
-CPPFLAGS = -I $(SMITHLAB_CPP)
-OPTFLAGS = -O3
-DEBUGFLAGS = -g
-
-COMPILER := $(shell $(CXX) --version)
-
-# clang++ -> add -lomp to link openmp
-ifneq '' '$(findstring clang, $(COMPILER))'
-	LDLIBS += lomp
-
-# GNU g++ -> add -fopenmp
-else ifneq '' '$(findstring g++, $(COMPILER))'
-	CXXFLAGS += -fopenmp
-endif
-
-LIBDEPS = $(STATIC_LIB) $(addprefix $(SMITHLAB_CPP)/, libsmithlab_cpp.a)
-
-ifdef DEBUG
-CXXFLAGS += $(DEBUGFLAGS)
-else
-CXXFLAGS += $(OPTFLAGS)
-endif
-
-all: $(PROGS) $(LIBDEPS)
-install: $(PROGS)
-	@mkdir -p $(SRC_ROOT)/bin
-	@install -m 755 $(PROGS) $(SRC_ROOT)/bin
-
-%.o: %.cpp %.hpp
-	$(CXX) $(CXXFLAGS) -c -o $@ $< $(CPPFLAGS)
-
-libabismal.a : $(STATIC_LIB)
-$(STATIC_LIB) : $(OBJECTS)
-	ar cr $(STATIC_LIB) $^
-
-$(BINARIES): $(LIBDEPS)
-
-%: %_main.cpp $(LIBDEPS)
-	$(CXX) $(CXXFLAGS) -o $@ $^ $(CPPFLAGS) $(LDLIBS)
-
-clean:
-	@-rm -f $(PROGS) $(STATIC_LIB) *.o *.so *.a *~
-.PHONY: clean