diff --git a/.gitignore b/.gitignore
index a7fc846..be8f01f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,5 @@ src/*.o
 .vscode/settings.json
 .gitignore
 v1.0.zip
+*.gch
+src/AlcoR
diff --git a/src/Makefile b/src/Makefile
index e46544f..6158bfc 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -1,110 +1,6 @@
 <<<<<<< HEAD
 # CMAKE generated file: DO NOT EDIT!
 # Generated by "Unix Makefiles" Generator, CMake Version 3.16
-=======
-#============================================================================#
-#
-#	AlcoR 2023 IEETA/DETI, UNIVERSITY OF AVEIRO
-#
-#============================================================================#
-BIN    = .
-CC     = gcc
-CPLP   =
-#-----------------------------------------------------------------------------
-CFLAGS = -Wall -Ofast -march=native -mtune=native $(CPLP)
-#-----------------------------------------------------------------------------
-LIBS   = -lm
-DEPS   = defs.h mem.h
-ALCOR_DEPS = keys.h msg.h dna.h param.h common.h levels.h strings.h lr.h si.h ex.h vi.h
-ALHABET_DEPS = common.h
-CM_DEPS = dna.h msg.h common.h alphabet.h tolerant.h rand.h carray.h buffer.h pmodels.h chash.h
-COMMON_DEPS = msg.h 
-DIST_DEPS = common.h alphabet.h
-DNA_DEPS = common.h msg.h 
-EX_DEPS = dna.h msg.h buffer.h common.h strings.h param.h
-KMER_DEPS = common.h dna.h 
-LEVELS_DEPS = msg.h
-LR_DEPS = threads.h msg.h dna.h buffer.h levels.h param.h alphabet.h common.h cache.h positions.h pmodels.h strings.h cm.h
-PAINT_DEPS = common.h msg.h 
-PARAM_DEPS = common.h msg.h dna.h strings.h keys.h alphabet.h
-PMODELS_DEPS = math.h common.h
-SI_DEPS = cm.h dna.h msg.h rand.h buffer.h common.h strings.h param.h
-STRINGS_DEPS = msg.h
-TOLERANT_DEPS = strings.h pmodels.h buffer.h
-VI_DEPS = dna.h msg.h buffer.h common.h strings.h param.h paint.h
-IF_DEPS = dna.h msg.h buffer.h common.h strings.h param.h
-PROG = $(BIN)/AlcoR
-OBJS = mem.o positions.o stats.o rand.o math.o buffer.o chash.o carray.o \
-		cache.o filter.o keys.o msg.o strings.o common.o alphabet.o dist.o \
-		dna.o kmer.o levels.o ex.o paint.o param.o pmodels.o tolerant.o if.o cm.o vi.o lr.o si.o
-#-----------------------------------------------------------------------------
-
-all:
-	$(MAKE) progs
-
-progs: $(PROG)
-$(BIN)/AlcoR: alcor.c $(DEPS) $(OBJS)
-	$(CC) $(CFLAGS) -o $(BIN)/AlcoR alcor.c $(OBJS) $(LIBS)
-
-alphabet.o: alphabet.c alphabet.h $(DEPS) $(ALHABET_DEPS)
-	$(CC) -c $(CFLAGS) alphabet.c
-buffer.o: buffer.c buffer.h $(DEPS)
-	$(CC) -c $(CFLAGS) buffer.c
-cache.o: cache.c cache.h $(DEPS)
-	$(CC) -c $(CFLAGS) cache.c
-carray.o: carray.c carray.h $(DEPS)
-	$(CC) -c $(CFLAGS) carray.c
-chash.o: chash.c chash.h $(DEPS)
-	$(CC) -c $(CFLAGS) chash.c
-cm.o: cm.c cm.h $(DEPS) $(CM_DEPS)
-	$(CC) -c $(CFLAGS) cm.c
-common.o: common.c common.h $(DEPS) $(COMMON_DEPS)
-	$(CC) -c $(CFLAGS) common.c
-dna.o: dna.c dna.h $(DEPS) $(DNA_DEPS)
-	$(CC) -c $(CFLAGS) dna.c
-dist.o: dist.c dist.h $(DEPS) $(DIST_DEPS)
-	$(CC) -c $(CFLAGS) dist.c
-ex.o: ex.c ex.h $(DEPS) $(EX_DEPS)
-	$(CC) -c $(CFLAGS) ex.c
-filter.o: filter.c filter.h $(DEPS)
-	$(CC) -c $(CFLAGS) filter.c
-if.o: if.c if.h $(DEPS) $(IF_DEPS)
-	$(CC) -c $(CFLAGS) if.c 
-keys.o: keys.c keys.h $(DEPS)
-	$(CC) -c $(CFLAGS) keys.c
-kmer.o: kmer.c kmer.h $(DEPS) $(KMER_DEPS)
-	$(CC) -c $(CFLAGS) kmer.c
-levels.o: levels.c levels.h $(DEPS) $(LEVELS_DEPS)
-	$(CC) -c $(CFLAGS) levels.c
-lr.o: lr.c lr.h threads.h $(DEPS) $(LR_DEPS)
-	$(CC) -c $(CFLAGS) lr.c
-math.o: math.c math.h $(DEPS)
-	$(CC) -c $(CFLAGS) math.c
-mem.o: mem.c mem.h $(DEPS)
-	$(CC) -c $(CFLAGS) mem.c
-msg.o: msg.c msg.h colors.h keys.h $(DEPS)
-	$(CC) -c $(CFLAGS) msg.c
-paint.o: paint.c paint.h $(DEPS) $(PAINT_DEPS)
-	$(CC) -c $(CFLAGS) paint.c
-param.o: param.c param.h $(DEPS) $(PARAM_DEPS)
-	$(CC) -c $(CFLAGS) param.c
-pmodels.o: pmodels.c pmodels.h $(DEPS) $(PMODELS_DEPS)
-	$(CC) -c $(CFLAGS) pmodels.c
-positions.o: positions.c positions.h $(DEPS)
-	$(CC) -c $(CFLAGS) positions.c
-rand.o: rand.c rand.h $(DEPS)
-	$(CC) -c $(CFLAGS) rand.c
-si.o: si.c si.h $(DEPS) $(SI_DEPS)
-	$(CC) -c $(CFLAGS) si.c
-stats.o: stats.c stats.h $(DEPS)
-	$(CC) -c $(CFLAGS) stats.c
-strings.o: strings.c strings.h $(DEPS) $(STRINGS_DEPS)
-	$(CC) -c $(CFLAGS) strings.c
-tolerant.o: tolerant.c tolerant.h $(DEPS) $(TOLERANT_DEPS)
-	$(CC) -c $(CFLAGS) tolerant.c
-vi.o: vi.c vi.h $(DEPS) $(VI_DEPS)
-	$(CC) -c $(CFLAGS) vi.c
->>>>>>> 6d556da0c81b8f814d045478c520a6d563f91fc6
 
 # Default target executed when no arguments are given to make.
 default_target: all
diff --git a/src/MakefileConda b/src/MakefileConda
new file mode 100644
index 0000000..ee31a4c
--- /dev/null
+++ b/src/MakefileConda
@@ -0,0 +1,134 @@
+#============================================================================#
+#
+#	AlcoR 2023 IEETA/DETI, UNIVERSITY OF AVEIRO
+#
+#============================================================================#
+BIN    = .
+CC     = gcc
+CPLP   =
+#-----------------------------------------------------------------------------
+CFLAGS = -Wall -Ofast -march=native -mtune=native $(CPLP)
+#-----------------------------------------------------------------------------
+LIBS   = -lm
+DEPS   = defs.h mem.h
+ALCOR_DEPS = keys.h msg.h dna.h param.h common.h levels.h strings.h lr.h si.h ex.h vi.h
+ALHABET_DEPS = common.h
+CM_DEPS = dna.h msg.h common.h alphabet.h tolerant.h rand.h carray.h buffer.h pmodels.h chash.h
+COMMON_DEPS = msg.h 
+DIST_DEPS = common.h alphabet.h
+DNA_DEPS = common.h msg.h 
+EX_DEPS = dna.h msg.h buffer.h common.h strings.h param.h
+KMER_DEPS = common.h dna.h 
+LEVELS_DEPS = msg.h
+LR_DEPS = threads.h msg.h dna.h buffer.h levels.h param.h alphabet.h common.h cache.h positions.h pmodels.h strings.h cm.h
+PAINT_DEPS = common.h msg.h 
+PARAM_DEPS = common.h msg.h dna.h strings.h keys.h alphabet.h
+PMODELS_DEPS = math.h common.h
+SI_DEPS = cm.h dna.h msg.h rand.h buffer.h common.h strings.h param.h
+STRINGS_DEPS = msg.h
+TOLERANT_DEPS = strings.h pmodels.h buffer.h
+VI_DEPS = dna.h msg.h buffer.h common.h strings.h param.h paint.h
+IF_DEPS = dna.h msg.h buffer.h common.h strings.h param.h
+PROG = $(BIN)/AlcoR
+OBJS = mem.o positions.o stats.o rand.o math.o buffer.o chash.o carray.o \
+	    cache.o filter.o keys.o msg.o strings.o common.o alphabet.o dist.o \
+	    dna.o kmer.o levels.o ex.o paint.o param.o pmodels.o tolerant.o if.o cm.o vi.o lr.o si.o
+#-----------------------------------------------------------------------------
+
+all: progs
+
+progs: $(PROG)
+$(BIN)/AlcoR: alcor.c $(DEPS) $(OBJS)
+	$(CC) $(CFLAGS) -o $(BIN)/AlcoR alcor.c $(OBJS) $(LIBS)
+
+alphabet.o: alphabet.c alphabet.h $(DEPS) $(ALHABET_DEPS)
+	$(CC) -c $(CFLAGS) alphabet.c
+
+buffer.o: buffer.c buffer.h $(DEPS)
+	$(CC) -c $(CFLAGS) buffer.c
+
+cache.o: cache.c cache.h $(DEPS)
+	$(CC) -c $(CFLAGS) cache.c
+
+carray.o: carray.c carray.h $(DEPS)
+	$(CC) -c $(CFLAGS) carray.c
+
+chash.o: chash.c chash.h $(DEPS)
+	$(CC) -c $(CFLAGS) chash.c
+
+cm.o: cm.c cm.h $(DEPS) $(CM_DEPS)
+	$(CC) -c $(CFLAGS) cm.c
+
+common.o: common.c common.h $(DEPS) $(COMMON_DEPS)
+	$(CC) -c $(CFLAGS) common.c
+
+defs.o: defs.c defs.h $(DEPS)
+	$(CC) -c $(CFLAGS) defs.c
+
+dist.o: dist.c dist.h $(DEPS) $(DIST_DEPS)
+	$(CC) -c $(CFLAGS) dist.c
+
+dna.o: dna.c dna.h $(DEPS) $(DNA_DEPS)
+	$(CC) -c $(CFLAGS) dna.c
+
+ex.o: ex.c ex.h $(DEPS) $(EX_DEPS)
+	$(CC) -c $(CFLAGS) ex.c
+
+filter.o: filter.c filter.h $(DEPS)
+	$(CC) -c $(CFLAGS) filter.c
+
+if.o: if.c if.h $(DEPS) $(IF_DEPS)
+	$(CC) -c $(CFLAGS) if.c
+
+kmer.o: kmer.c kmer.h $(DEPS) $(KMER_DEPS)
+	$(CC) -c $(CFLAGS) kmer.c
+
+keys.o: keys.c keys.h $(DEPS)
+	$(CC) -c $(CFLAGS) keys.c
+
+levels.o: levels.c levels.h $(DEPS) $(LEVELS_DEPS)
+	$(CC) -c $(CFLAGS) levels.c
+
+lr.o: lr.c lr.h $(DEPS) $(LR_DEPS)
+	$(CC) -c $(CFLAGS) lr.c
+
+math.o: math.c math.h $(DEPS)
+	$(CC) -c $(CFLAGS) math.c
+
+mem.o: mem.c mem.h $(DEPS)
+	$(CC) -c $(CFLAGS) mem.c
+
+msg.o: msg.c msg.h $(DEPS)
+	$(CC) -c $(CFLAGS) msg.c
+
+paint.o: paint.c paint.h $(DEPS) $(PAINT_DEPS)
+	$(CC) -c $(CFLAGS) paint.c
+
+param.o: param.c param.h $(DEPS) $(PARAM_DEPS)
+	$(CC) -c $(CFLAGS) param.c
+
+pmodels.o: pmodels.c pmodels.h $(DEPS) $(PMODELS_DEPS)
+	$(CC) -c $(CFLAGS) pmodels.c
+
+positions.o: positions.c positions.h $(DEPS)
+	$(CC) -c $(CFLAGS) positions.c
+
+rand.o: rand.c rand.h $(DEPS)
+	$(CC) -c $(CFLAGS) rand.c
+
+si.o: si.c si.h $(DEPS) $(SI_DEPS)
+	$(CC) -c $(CFLAGS) si.c
+
+stats.o: stats.c stats.h $(DEPS)
+	$(CC) -c $(CFLAGS) stats.c
+
+strings.o: strings.c strings.h $(DEPS) $(STRINGS_DEPS)
+	$(CC) -c $(CFLAGS) strings.c
+
+tolerant.o: tolerant.c tolerant.h $(DEPS) $(TOLERANT_DEPS)
+	$(CC) -c $(CFLAGS) tolerant.c
+
+vi.o: vi.c vi.h $(DEPS) $(VI_DEPS)
+	$(CC) -c $(CFLAGS) vi.c
+
+