diff --git a/Debug/.gdb_history b/Debug/.gdb_history
deleted file mode 100644
index 942574c..0000000
--- a/Debug/.gdb_history
+++ /dev/null
@@ -1,62 +0,0 @@
-r  -1acghtgd -2gctcagctagcta /Users/coissac/encours/ecoPCR/tools/ecodb 
-print put
-print out
-f ecoPCR
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-bt
-print label1
-up
-print label1
-print (char*)label1
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-bt
-up 3
-l
-b 38
-r
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print label
-print ranks
-print *ranks
-print ranks->label +1
-print *ranks->label +1
-print *(ranks->label +1)
-print *(ranks->label +2)
-b ecotax.c:147
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print current_taxon ;
-print current_taxon 
-n
-print current_taxon ;
-print current_taxon 
-print *current_taxon 
-print taxonomy->taxons[11]
-print taxonomy->taxons[2952]
-print taxonomy->taxons->taxon[2952]
-print taxonomy->ranks->rank[11]
-print taxonomy->ranks->label[11]
-print taxonomy->ranks->label[3]
-b ecotax.c:147
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print current_taxon 
-print *current_taxon 
-n
-print *current_taxon 
-b ecotax.c:147
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-n
-print *current_taxon 
-r  -1GGGCAATCCTGAGCCAA -2CCATTGAGTCTCTGCACCTATC -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-n
-print *current_taxon 
-b ecodna.c:70
-r  -1GGGCAATCCTGAGCC#A#A# -2CCATTGAGTCTCTGCACCTA#T#C# -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-*sb
-print *sb
-print sb
-print str
-b 52
-r  -1GGGCAATCCTGAGCC#A#A# -2CCATTGAGTCTCTGCACCTA#T#C# -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-print str
-r  -1GGGCAATCCTGAGCC#A#A# -2CCATTGAGTCTCTGCACCTA#T#C# -l5 -L200 -e2 /Users/coissac/encours/ecoPCR/tools/ecodb
-bt
diff --git a/Debug/makefile b/Debug/makefile
deleted file mode 100644
index 2c69725..0000000
--- a/Debug/makefile
+++ /dev/null
@@ -1,46 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
--include ../makefile.init
-
-RM := rm -rf
-
-# All of the sources participating in the build are defined here
--include sources.mk
--include subdir.mk
--include src/libecoPCR/subdir.mk
--include src/libapat/subdir.mk
--include src/subdir.mk
--include objects.mk
-
-ifneq ($(MAKECMDGOALS),clean)
-ifneq ($(strip $(C_DEPS)),)
--include $(C_DEPS)
-endif
-endif
-
--include ../makefile.defs
-
-# Add inputs and outputs from these tool invocations to the build variables 
-
-# All Target
-all: ecoPCR
-
-# Tool invocations
-ecoPCR: $(OBJS) $(USER_OBJS)
-	@echo 'Building target: $@'
-	@echo 'Invoking: MacOS X C Linker'
-	gcc  -o "ecoPCR" $(OBJS) $(USER_OBJS) $(LIBS)
-	@echo 'Finished building target: $@'
-	@echo ' '
-
-# Other Targets
-clean:
-	-$(RM) $(OBJS)$(EXECUTABLES)$(C_DEPS) ecoPCR
-	-@echo ' '
-
-.PHONY: all clean dependents
-.SECONDARY:
-
--include ../makefile.targets
diff --git a/Debug/objects.mk b/Debug/objects.mk
deleted file mode 100644
index 899fd62..0000000
--- a/Debug/objects.mk
+++ /dev/null
@@ -1,7 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-LIBS := -lz
-
-USER_OBJS :=
\ No newline at end of file
diff --git a/Debug/sources.mk b/Debug/sources.mk
deleted file mode 100644
index eb1bf94..0000000
--- a/Debug/sources.mk
+++ /dev/null
@@ -1,19 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-C_SRCS := 
-O_SRCS := 
-ASM_SRCS := 
-S_SRCS := 
-OBJ_SRCS := 
-OBJS := 
-EXECUTABLES := 
-C_DEPS := 
-
-# Every subdirectory with source files must be described here
-SUBDIRS := \
-src/libecoPCR \
-src/libapat \
-src \
-
diff --git a/Debug/src/libapat/CODES/subdir.mk b/Debug/src/libapat/CODES/subdir.mk
deleted file mode 100644
index a769d35..0000000
--- a/Debug/src/libapat/CODES/subdir.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libapat/CODES/gendual.c 
-
-OBJS += \
-./src/libapat/CODES/gendual.o 
-
-C_DEPS += \
-./src/libapat/CODES/gendual.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libapat/CODES/%.o: ../src/libapat/CODES/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-
diff --git a/Debug/src/libapat/subdir.mk b/Debug/src/libapat/subdir.mk
deleted file mode 100644
index 1ba3c9a..0000000
--- a/Debug/src/libapat/subdir.mk
+++ /dev/null
@@ -1,30 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libapat/apat_parse.c \
-../src/libapat/apat_search.c \
-../src/libapat/libstki.c 
-
-OBJS += \
-./src/libapat/apat_parse.o \
-./src/libapat/apat_search.o \
-./src/libapat/libstki.o 
-
-C_DEPS += \
-./src/libapat/apat_parse.d \
-./src/libapat/apat_search.d \
-./src/libapat/libstki.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libapat/%.o: ../src/libapat/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-
diff --git a/Debug/src/libecoPCR/subdir.mk b/Debug/src/libecoPCR/subdir.mk
deleted file mode 100644
index 35eef17..0000000
--- a/Debug/src/libecoPCR/subdir.mk
+++ /dev/null
@@ -1,45 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libecoPCR/ecoError.c \
-../src/libecoPCR/ecoIOUtils.c \
-../src/libecoPCR/ecoMalloc.c \
-../src/libecoPCR/ecoapat.c \
-../src/libecoPCR/ecodna.c \
-../src/libecoPCR/ecorank.c \
-../src/libecoPCR/ecoseq.c \
-../src/libecoPCR/ecotax.c 
-
-OBJS += \
-./src/libecoPCR/ecoError.o \
-./src/libecoPCR/ecoIOUtils.o \
-./src/libecoPCR/ecoMalloc.o \
-./src/libecoPCR/ecoapat.o \
-./src/libecoPCR/ecodna.o \
-./src/libecoPCR/ecorank.o \
-./src/libecoPCR/ecoseq.o \
-./src/libecoPCR/ecotax.o 
-
-C_DEPS += \
-./src/libecoPCR/ecoError.d \
-./src/libecoPCR/ecoIOUtils.d \
-./src/libecoPCR/ecoMalloc.d \
-./src/libecoPCR/ecoapat.d \
-./src/libecoPCR/ecodna.d \
-./src/libecoPCR/ecorank.d \
-./src/libecoPCR/ecoseq.d \
-./src/libecoPCR/ecotax.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libecoPCR/%.o: ../src/libecoPCR/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-
diff --git a/Debug/src/subdir.mk b/Debug/src/subdir.mk
deleted file mode 100644
index 8a80215..0000000
--- a/Debug/src/subdir.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/ecopcr.c 
-
-OBJS += \
-./src/ecopcr.o 
-
-C_DEPS += \
-./src/ecopcr.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/%.o: ../src/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-
diff --git a/Release/makefile b/Release/makefile
deleted file mode 100644
index 2c69725..0000000
--- a/Release/makefile
+++ /dev/null
@@ -1,46 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
--include ../makefile.init
-
-RM := rm -rf
-
-# All of the sources participating in the build are defined here
--include sources.mk
--include subdir.mk
--include src/libecoPCR/subdir.mk
--include src/libapat/subdir.mk
--include src/subdir.mk
--include objects.mk
-
-ifneq ($(MAKECMDGOALS),clean)
-ifneq ($(strip $(C_DEPS)),)
--include $(C_DEPS)
-endif
-endif
-
--include ../makefile.defs
-
-# Add inputs and outputs from these tool invocations to the build variables 
-
-# All Target
-all: ecoPCR
-
-# Tool invocations
-ecoPCR: $(OBJS) $(USER_OBJS)
-	@echo 'Building target: $@'
-	@echo 'Invoking: MacOS X C Linker'
-	gcc  -o "ecoPCR" $(OBJS) $(USER_OBJS) $(LIBS)
-	@echo 'Finished building target: $@'
-	@echo ' '
-
-# Other Targets
-clean:
-	-$(RM) $(OBJS)$(EXECUTABLES)$(C_DEPS) ecoPCR
-	-@echo ' '
-
-.PHONY: all clean dependents
-.SECONDARY:
-
--include ../makefile.targets
diff --git a/Release/objects.mk b/Release/objects.mk
deleted file mode 100644
index 899fd62..0000000
--- a/Release/objects.mk
+++ /dev/null
@@ -1,7 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-LIBS := -lz
-
-USER_OBJS :=
\ No newline at end of file
diff --git a/Release/sources.mk b/Release/sources.mk
deleted file mode 100644
index eb1bf94..0000000
--- a/Release/sources.mk
+++ /dev/null
@@ -1,19 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-C_SRCS := 
-O_SRCS := 
-ASM_SRCS := 
-S_SRCS := 
-OBJ_SRCS := 
-OBJS := 
-EXECUTABLES := 
-C_DEPS := 
-
-# Every subdirectory with source files must be described here
-SUBDIRS := \
-src/libecoPCR \
-src/libapat \
-src \
-
diff --git a/Release/src/libapat/subdir.mk b/Release/src/libapat/subdir.mk
deleted file mode 100644
index 44cfe8f..0000000
--- a/Release/src/libapat/subdir.mk
+++ /dev/null
@@ -1,30 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libapat/apat_parse.c \
-../src/libapat/apat_search.c \
-../src/libapat/libstki.c 
-
-OBJS += \
-./src/libapat/apat_parse.o \
-./src/libapat/apat_search.o \
-./src/libapat/libstki.o 
-
-C_DEPS += \
-./src/libapat/apat_parse.d \
-./src/libapat/apat_search.d \
-./src/libapat/libstki.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libapat/%.o: ../src/libapat/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-
diff --git a/Release/src/libecoPCR/subdir.mk b/Release/src/libecoPCR/subdir.mk
deleted file mode 100644
index 59b89c3..0000000
--- a/Release/src/libecoPCR/subdir.mk
+++ /dev/null
@@ -1,45 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/libecoPCR/ecoError.c \
-../src/libecoPCR/ecoIOUtils.c \
-../src/libecoPCR/ecoMalloc.c \
-../src/libecoPCR/ecoapat.c \
-../src/libecoPCR/ecodna.c \
-../src/libecoPCR/ecorank.c \
-../src/libecoPCR/ecoseq.c \
-../src/libecoPCR/ecotax.c 
-
-OBJS += \
-./src/libecoPCR/ecoError.o \
-./src/libecoPCR/ecoIOUtils.o \
-./src/libecoPCR/ecoMalloc.o \
-./src/libecoPCR/ecoapat.o \
-./src/libecoPCR/ecodna.o \
-./src/libecoPCR/ecorank.o \
-./src/libecoPCR/ecoseq.o \
-./src/libecoPCR/ecotax.o 
-
-C_DEPS += \
-./src/libecoPCR/ecoError.d \
-./src/libecoPCR/ecoIOUtils.d \
-./src/libecoPCR/ecoMalloc.d \
-./src/libecoPCR/ecoapat.d \
-./src/libecoPCR/ecodna.d \
-./src/libecoPCR/ecorank.d \
-./src/libecoPCR/ecoseq.d \
-./src/libecoPCR/ecotax.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/libecoPCR/%.o: ../src/libecoPCR/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-
diff --git a/Release/src/subdir.mk b/Release/src/subdir.mk
deleted file mode 100644
index f317992..0000000
--- a/Release/src/subdir.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-################################################################################
-# Automatically-generated file. Do not edit!
-################################################################################
-
-# Add inputs and outputs from these tool invocations to the build variables 
-C_SRCS += \
-../src/ecopcr.c 
-
-OBJS += \
-./src/ecopcr.o 
-
-C_DEPS += \
-./src/ecopcr.d 
-
-
-# Each subdirectory must supply rules for building sources it contributes
-src/%.o: ../src/%.c
-	@echo 'Building file: $<'
-	@echo 'Invoking: GCC C Compiler'
-	gcc -DMAC_OS_X -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.d)" -o"$@" "$<"
-	@echo 'Finished building: $<'
-	@echo ' '
-
-