diff --git a/README.md b/README.md
index 1d6d329f..54d7cc5c 100644
--- a/README.md
+++ b/README.md
@@ -45,6 +45,35 @@ At the moment, GLIMPSE2 performs imputation only from a reference panel of sampl
 
 To build the source code, please refer to the [step-by-step guide on the website](https://odelaneau.github.io/GLIMPSE/docs/installation).
 
+#### Building on macOS
+
+GLIMPSE2 supports macOS builds, including Apple Silicon (ARM64) devices. The build system automatically detects dependencies installed via Homebrew.
+
+**Prerequisites:**
+```bash
+# Install dependencies via Homebrew
+brew install boost htslib openssl@3 libdeflate
+```
+
+**Building:**
+```bash
+# Build all tools
+make
+
+# Or build individual tools
+make phase
+make chunk
+make ligate
+make split_reference
+make concordance
+```
+
+**Platform-specific notes:**
+
+- **⚠️ Performance Note (WIP):** On Apple Silicon and other ARM platforms, GLIMPSE2 currently uses scalar fallback implementations instead of AVX2 SIMD instructions. This means **significantly slower performance** compared to x86_64 with AVX2. Native ARM NEON optimizations are planned for future releases.
+- On x86_64 platforms, native AVX2/FMA instructions are used for optimal performance
+- The build system automatically detects the architecture and applies appropriate compiler flags
+
 #### Docker images
 
 ##### Dockerhub
diff --git a/chunk/makefile b/chunk/makefile
index f6fafcb0..4aeba3dd 100644
--- a/chunk/makefile
+++ b/chunk/makefile
@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 	
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)
diff --git a/concordance/makefile b/concordance/makefile
index f6fafcb0..4aeba3dd 100644
--- a/concordance/makefile
+++ b/concordance/makefile
@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 	
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)
diff --git a/ligate/makefile b/ligate/makefile
index f6fafcb0..4aeba3dd 100644
--- a/ligate/makefile
+++ b/ligate/makefile
@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 	
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)
diff --git a/makefile b/makefile
index 5896d32c..d8b5e5d7 100644
--- a/makefile
+++ b/makefile
@@ -1,14 +1,23 @@
 projects = chunk concordance ligate phase split_reference
 
-.PHONY: all $(projects)
+BOOST_INC := $(shell brew --prefix boost)/include
+BOOST_LIB := $(shell brew --prefix boost)/lib
+
+CXXFLAGS += -I$(BOOST_INC)
+LDFLAGS  += -L$(BOOST_LIB)
+LDLIBS   += -lboost_program_options
+
+.PHONY: all $(projects) clean
 
 all: $(projects)
 
 $(projects):
-	$(MAKE) -C $@ $(COMPILATION_ENV)
+	$(MAKE) -C $@ $(COMPILATION_ENV) \
+		CXXFLAGS="$(CXXFLAGS)" \
+		LDFLAGS="$(LDFLAGS)" \
+		LDLIBS="$(LDLIBS)"
 
 clean:
 	for dir in $(projects); do \
-	$(MAKE) $@ -C $$dir; \
+		$(MAKE) -C $$dir clean; \
 	done
-
diff --git a/phase/makefile b/phase/makefile
index f6fafcb0..eee9ced3 100644
--- a/phase/makefile
+++ b/phase/makefile
@@ -9,12 +9,14 @@ dummy_build_folder_obj := $(shell mkdir -p obj)
 #COMPILER & LINKER FLAGS
 CXXFLAG=-O3 -Wno-ignored-attributes
 LDFLAG=-O3
+HOST_ARCH := $(shell uname -m)
 
 #CXXFLAG=-O0 -g -Wno-ignored-attributes
 #LDFLAG=-O0
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,13 +27,45 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib-1.17)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib-1.17/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
 #CXXFLAG+= -D__COMMIT_DATE__=\"$(COMMIT_DATE)\"
 
 ifeq ($(NAME),phase)
- CXXFLAG+=-mavx2 -mfma
+ ifeq ($(HOST_ARCH),x86_64)
+  CXXFLAG+=-mavx2 -mfma
+ else
+  $(info Skipping AVX2/FMA flags for architecture $(HOST_ARCH))
+ endif
 endif
 
 COMMIT_VERS=3bed6d9
@@ -147,10 +181,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 	
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)
diff --git a/phase/src/models/imputation_hmm.h b/phase/src/models/imputation_hmm.h
index 1bda64cb..deadfd1c 100644
--- a/phase/src/models/imputation_hmm.h
+++ b/phase/src/models/imputation_hmm.h
@@ -28,7 +28,7 @@
 
 #include <utils/otools.h>
 #include <containers/conditioning_set.h>
-#include <immintrin.h>
+#include "simd_compat.h"
 #include <boost/align/aligned_allocator.hpp>
 
 template <typename T>
diff --git a/phase/src/models/phasing_hmm.h b/phase/src/models/phasing_hmm.h
index 26172473..82f5273a 100644
--- a/phase/src/models/phasing_hmm.h
+++ b/phase/src/models/phasing_hmm.h
@@ -28,7 +28,7 @@
 
 #include <utils/otools.h>
 #include <containers/conditioning_set.h>
-#include <immintrin.h>
+#include "simd_compat.h"
 #include <boost/align/aligned_allocator.hpp>
 
 template <typename T>
diff --git a/phase/src/models/simd_compat.h b/phase/src/models/simd_compat.h
new file mode 100644
index 00000000..34a0f3e6
--- /dev/null
+++ b/phase/src/models/simd_compat.h
@@ -0,0 +1,233 @@
+#pragma once
+
+// SIMD compatibility layer to allow building on platforms without AVX2
+// support (for example, Apple Silicon). When AVX is available we defer to
+// the native intrinsics, otherwise we provide a scalar fallback that mimics
+// the API used by the GLIMPSE models.
+//
+// ⚠️  PERFORMANCE NOTE (WIP):
+// The scalar fallback implementation is SIGNIFICANTLY SLOWER than native AVX2.
+// This is a functional implementation to enable compilation on ARM platforms,
+// but performance optimization using ARM NEON intrinsics is planned for future
+// releases. Users on Apple Silicon should expect reduced performance compared
+// to x86_64 systems with AVX2 support.
+
+#if defined(__AVX2__) || defined(__AVX__)
+  #include <immintrin.h>
+  #define GLIMPSE_SIMD_HAS_AVX 1
+#else
+  #define GLIMPSE_SIMD_HAS_AVX 0
+  #include <algorithm>
+  #include <array>
+  #include <cstdint>
+  #include <cstring>
+
+  namespace glimpse::simd
+  {
+    struct alignas(32) Vec256f {
+      float data[8];
+    };
+
+    struct alignas(32) Vec256i {
+      std::uint32_t data[8];
+    };
+
+    struct alignas(16) Vec128f {
+      float data[4];
+    };
+
+    template <typename T>
+    inline T bit_cast_copy(const void* src)
+    {
+      T dst;
+      std::memcpy(&dst, src, sizeof(T));
+      return dst;
+    }
+
+    template <typename T>
+    inline void bit_copy_to(const T& src, void* dst)
+    {
+      std::memcpy(dst, &src, sizeof(T));
+    }
+  }
+
+  using __m256  = glimpse::simd::Vec256f;
+  using __m256i = glimpse::simd::Vec256i;
+  using __m128  = glimpse::simd::Vec128f;
+
+  // Floating point helpers -------------------------------------------------
+  inline __m256 _mm256_set1_ps(float value)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i) result.data[i] = value;
+    return result;
+  }
+
+  inline __m256 _mm256_load_ps(const float* ptr)
+  {
+    return glimpse::simd::bit_cast_copy<__m256>(ptr);
+  }
+
+  inline void _mm256_store_ps(float* ptr, const __m256& value)
+  {
+    glimpse::simd::bit_copy_to(value, ptr);
+  }
+
+  inline __m256 _mm256_add_ps(const __m256& a, const __m256& b)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i) result.data[i] = a.data[i] + b.data[i];
+    return result;
+  }
+
+  inline __m256 _mm256_mul_ps(const __m256& a, const __m256& b)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i) result.data[i] = a.data[i] * b.data[i];
+    return result;
+  }
+
+  inline __m256 _mm256_div_ps(const __m256& a, const __m256& b)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i) result.data[i] = a.data[i] / b.data[i];
+    return result;
+  }
+
+  inline __m256 _mm256_max_ps(const __m256& a, const __m256& b)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i) result.data[i] = std::max(a.data[i], b.data[i]);
+    return result;
+  }
+
+  inline __m256 _mm256_min_ps(const __m256& a, const __m256& b)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i) result.data[i] = std::min(a.data[i], b.data[i]);
+    return result;
+  }
+
+  inline __m256 _mm256_fmadd_ps(const __m256& a, const __m256& b, const __m256& c)
+  {
+    return _mm256_add_ps(_mm256_mul_ps(a, b), c);
+  }
+
+  inline __m256 _mm256_setzero_ps()
+  {
+    return _mm256_set1_ps(0.0f);
+  }
+
+  // Integer helpers --------------------------------------------------------
+  inline __m256i _mm256_set1_epi32(int value)
+  {
+    __m256i result;
+    std::uint32_t converted = static_cast<std::uint32_t>(value);
+    for (int i = 0; i < 8; ++i) result.data[i] = converted;
+    return result;
+  }
+
+  inline __m256i _mm256_set_epi32(int e7, int e6, int e5, int e4, int e3, int e2, int e1, int e0)
+  {
+    __m256i result;
+    result.data[0] = static_cast<std::uint32_t>(e0);
+    result.data[1] = static_cast<std::uint32_t>(e1);
+    result.data[2] = static_cast<std::uint32_t>(e2);
+    result.data[3] = static_cast<std::uint32_t>(e3);
+    result.data[4] = static_cast<std::uint32_t>(e4);
+    result.data[5] = static_cast<std::uint32_t>(e5);
+    result.data[6] = static_cast<std::uint32_t>(e6);
+    result.data[7] = static_cast<std::uint32_t>(e7);
+    return result;
+  }
+
+  inline __m256i _mm256_sllv_epi32(const __m256i& values, const __m256i& counts)
+  {
+    __m256i result;
+    for (int i = 0; i < 8; ++i)
+    {
+      std::uint32_t shift = counts.data[i] & 31u;
+      result.data[i] = values.data[i] << shift;
+    }
+    return result;
+  }
+
+  inline __m256 _mm256_castsi256_ps(const __m256i& value)
+  {
+    return glimpse::simd::bit_cast_copy<__m256>(value.data);
+  }
+
+  inline __m256i _mm256_castps_si256(const __m256& value)
+  {
+    return glimpse::simd::bit_cast_copy<__m256i>(value.data);
+  }
+
+  inline __m256 _mm256_blendv_ps(const __m256& a, const __m256& b, const __m256& mask)
+  {
+    __m256 result;
+    for (int i = 0; i < 8; ++i)
+    {
+      std::uint32_t bits = glimpse::simd::bit_cast_copy<std::uint32_t>(&mask.data[i]);
+      result.data[i] = (bits & 0x80000000u) ? b.data[i] : a.data[i];
+    }
+    return result;
+  }
+
+  // Mixed helpers ----------------------------------------------------------
+  inline __m128 _mm256_castps256_ps128(const __m256& value)
+  {
+    __m128 result;
+    for (int i = 0; i < 4; ++i) result.data[i] = value.data[i];
+    return result;
+  }
+
+  inline __m128 _mm256_extractf128_ps(const __m256& value, const int index)
+  {
+    __m128 result;
+    const int offset = (index & 1) ? 4 : 0;
+    for (int i = 0; i < 4; ++i) result.data[i] = value.data[offset + i];
+    return result;
+  }
+
+  // SSE fallbacks ----------------------------------------------------------
+  inline __m128 _mm_add_ps(const __m128& a, const __m128& b)
+  {
+    __m128 result;
+    for (int i = 0; i < 4; ++i) result.data[i] = a.data[i] + b.data[i];
+    return result;
+  }
+
+  inline __m128 _mm_movehdup_ps(const __m128& a)
+  {
+    __m128 result;
+    result.data[0] = a.data[1];
+    result.data[1] = a.data[1];
+    result.data[2] = a.data[3];
+    result.data[3] = a.data[3];
+    return result;
+  }
+
+  inline __m128 _mm_movehl_ps(const __m128& a, const __m128& b)
+  {
+    __m128 result;
+    result.data[0] = b.data[2];
+    result.data[1] = b.data[3];
+    result.data[2] = a.data[2];
+    result.data[3] = a.data[3];
+    return result;
+  }
+
+  inline __m128 _mm_add_ss(const __m128& a, const __m128& b)
+  {
+    __m128 result = a;
+    result.data[0] = a.data[0] + b.data[0];
+    return result;
+  }
+
+  inline float _mm_cvtss_f32(const __m128& a)
+  {
+    return a.data[0];
+  }
+
+  // Convenience helpers ----------------------------------------------------
+  #endif  // GLIMPSE_SIMD_HAS_AVX
diff --git a/split_reference/makefile b/split_reference/makefile
index 4f8b0e36..1be33c3f 100644
--- a/split_reference/makefile
+++ b/split_reference/makefile
@@ -15,6 +15,7 @@ LDFLAG=-O3
 
 #DYNAMIC LIBRARIES
 DYN_LIBS=-lz -lpthread -lbz2 -llzma -lcurl -lcrypto -ldeflate
+BASE_DYN_LIBS := $(DYN_LIBS)
 
 HFILE=$(shell find src -name *.h)
 CFILE=$(shell find src -name *.cpp)
@@ -25,6 +26,34 @@ NAME=$(shell basename $(CURDIR))
 BFILE=bin/GLIMPSE2_$(NAME)
 EXEFILE=bin/GLIMPSE2_$(NAME)_static
 
+BREW_AVAILABLE := $(shell command -v brew 2>/dev/null)
+BOOST_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix boost 2>/dev/null),)
+HTSLIB_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix htslib 2>/dev/null),)
+
+BOOST_INC_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/include,)
+BOOST_LIB_DIR_AUTO := $(if $(BOOST_PREFIX_AUTO),$(BOOST_PREFIX_AUTO)/lib,)
+BOOST_LIB_IO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.a $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.dylib $(BOOST_LIB_DIR_AUTO)/libboost_iostreams.so))
+BOOST_LIB_PO_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_program_options.a $(BOOST_LIB_DIR_AUTO)/libboost_program_options.dylib $(BOOST_LIB_DIR_AUTO)/libboost_program_options.so))
+BOOST_LIB_SE_AUTO := $(firstword $(wildcard $(BOOST_LIB_DIR_AUTO)/libboost_serialization.a $(BOOST_LIB_DIR_AUTO)/libboost_serialization.dylib $(BOOST_LIB_DIR_AUTO)/libboost_serialization.so))
+
+HTSLIB_INC_AUTO := $(if $(HTSLIB_PREFIX_AUTO),$(HTSLIB_PREFIX_AUTO)/include,)
+HTSLIB_LIB_AUTO := $(firstword $(wildcard $(HTSLIB_PREFIX_AUTO)/lib/libhts.a $(HTSLIB_PREFIX_AUTO)/lib/libhts.dylib $(HTSLIB_PREFIX_AUTO)/lib/libhts.so))
+
+OPENSSL_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix openssl@3 2>/dev/null),)
+LIBDEFLATE_PREFIX_AUTO := $(if $(BREW_AVAILABLE),$(shell brew --prefix libdeflate 2>/dev/null),)
+
+EXTRA_LDFLAGS_AUTO := $(strip $(if $(BOOST_LIB_DIR_AUTO),-L$(BOOST_LIB_DIR_AUTO)) $(if $(HTSLIB_PREFIX_AUTO),-L$(HTSLIB_PREFIX_AUTO)/lib) $(if $(OPENSSL_PREFIX_AUTO),-L$(OPENSSL_PREFIX_AUTO)/lib) $(if $(LIBDEFLATE_PREFIX_AUTO),-L$(LIBDEFLATE_PREFIX_AUTO)/lib))
+
+DEFAULT_BOOST_INC := $(or $(BOOST_INC_AUTO),/usr/include)
+DEFAULT_BOOST_LIB_IO := $(or $(BOOST_LIB_IO_AUTO),-lboost_iostreams)
+DEFAULT_BOOST_LIB_PO := $(or $(BOOST_LIB_PO_AUTO),-lboost_program_options)
+DEFAULT_BOOST_LIB_SE := $(or $(BOOST_LIB_SE_AUTO),-lboost_serialization)
+
+DEFAULT_HTSLIB_INC := $(or $(HTSLIB_INC_AUTO),/home/srubinac/git/htslib)
+DEFAULT_HTSLIB_LIB := $(or $(HTSLIB_LIB_AUTO),/home/srubinac/git/htslib/libhts.a)
+
+.DEFAULT_GOAL := auto
+
 #COMMIT_VERS=$(shell git rev-parse --short HEAD)
 #COMMIT_DATE=$(shell git log -1 --format=%cd --date=short)
 #CXXFLAG+= -D__COMMIT_ID__=\"$(COMMIT_VERS)\"
@@ -147,10 +176,19 @@ static_exe: BOOST_LIB_SE=/usr/local/lib/libboost_serialization.a
 static_exe: $(EXEFILE)
 
 #COMPILATION RULES
-all: desktop
+all: auto
+
+auto: BOOST_INC=$(DEFAULT_BOOST_INC)
+auto: BOOST_LIB_IO=$(DEFAULT_BOOST_LIB_IO)
+auto: BOOST_LIB_PO=$(DEFAULT_BOOST_LIB_PO)
+auto: BOOST_LIB_SE=$(DEFAULT_BOOST_LIB_SE)
+auto: HTSLIB_INC=$(DEFAULT_HTSLIB_INC)
+auto: HTSLIB_LIB=$(DEFAULT_HTSLIB_LIB)
+auto: AUTO_LDFLAG=$(strip $(LDFLAG) $(EXTRA_LDFLAGS_AUTO))
+auto: $(BFILE)
 	
 $(BFILE): $(OFILE)
-	$(CXX) $(LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
+	$(CXX) $(AUTO_LDFLAG) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) $(BGEN_LIB) -o $@ $(DYN_LIBS)
 
 $(EXEFILE): $(OFILE)
 	$(CXX) $(LDFLAG) -static -static-libgcc -static-libstdc++ -pthread -o $(EXEFILE) $^ $(HTSLIB_LIB) $(BOOST_LIB_IO) $(BOOST_LIB_PO) $(BOOST_LIB_SE) -Wl,-Bstatic $(DYN_LIBS)