diff --git a/src/convertNR.cpp b/src/convertNR.cpp
index 394fc0c..48214ba 100644
--- a/src/convertNR.cpp
+++ b/src/convertNR.cpp
@@ -41,11 +41,12 @@ int main(int argc, char **argv) {
 	bool verbose = false;
 	bool debug = false;
 	bool addAcc = false;
+        bool all_taxa = false;
 
 	// --------------------- START ------------------------------------------------------------------
 	// Read command line params
 	int c;
-	while ((c = getopt(argc, argv, "ahdvrl:g:t:i:o:")) != -1) {
+	while ((c = getopt(argc, argv, "ahdvrAl:g:t:i:o:")) != -1) {
 		switch (c)  {
 			case 'h':
 				usage(argv[0]);
@@ -55,6 +56,8 @@ int main(int argc, char **argv) {
 				verbose = true; break;
 			case 'a':
 				addAcc = true; break;
+			case 'A':
+				all_taxa = true; break;
 			case 'l':
 				list_filename = optarg; break;
 			case 't':
@@ -84,7 +87,8 @@ int main(int argc, char **argv) {
 	parseNodesDmp(*nodes,nodes_file);
 	nodes_file.close();
 
-	if(list_filename.length()==0) {
+        if(all_taxa) {std::cerr << "Using all taxa, due to '-A' option." << std::endl;}
+	else if(list_filename.length()==0) {
 		std::cerr << "No taxa list specified, using Archaea, Bacteria, and Viruses." << std::endl;
 		include_ids.insert((uint64_t)2);
 		include_ids.insert((uint64_t)2157);
@@ -162,6 +166,9 @@ int main(int argc, char **argv) {
 		inputfile.open(nr_filename);
 		if(!inputfile.is_open()) { error("Could not open file " + nr_filename); exit(EXIT_FAILURE); }
 	}
+        else {
+                nr_filename = "std::cin";
+        }
 
 	if(verbose) std::cerr << "Writing to file " << out_filename << std::endl;
 	std::ofstream out_file;
@@ -209,7 +216,7 @@ int main(int argc, char **argv) {
 				if(nodes->count(lca)==0) { std::cerr << "Taxon ID " << lca << " not found in taxonomy!" << std::endl; continue; }
 				uint64_t id = lca;
 				while(nodes->count(id)>0 && id != 1) {
-					if(include_ids.count(id) > 0) {
+					if(all_taxa || include_ids.count(id) > 0) {
 						keep = true;
 						break;
 					}
@@ -264,6 +271,7 @@ void usage(char *progname) {
 	fprintf(stderr, "   -o FILENAME   Name of output file.\n");
 	fprintf(stderr, "Optional arguments:\n");
 	fprintf(stderr, "   -a            Prefix taxon ID in database names with the first Accession.Ver\n");
+	fprintf(stderr, "   -A            Use all taxids. This overrides -l and the default (only Archaea, Bacteria, and Viruses)\n");
 	fprintf(stderr, "   -i FILENAME   Name of NR file. If this option is not used, then the program will read from STDIN.\n");
 	fprintf(stderr, "   -l FILENAME   Name of file containing IDs of taxa that will be extracted from the NR file. The IDs must be contained in nodes.dmp.\n");
 	exit(EXIT_FAILURE);
diff --git a/src/makefile b/src/makefile
index fedc140..ef35c6a 100644
--- a/src/makefile
+++ b/src/makefile
@@ -73,10 +73,13 @@ convertNR: makefile bwt/mkbwt Config.o convertNR.o util.o $(BLASTOBJS)
 
 
 clean:
-	rm -f -v bwt/mkbwt bwt/mkfmi kaiju kaijux kaijup kaiju2krona mergeOutputs kaijuReport convertNR addTaxonNames ../bin/*
+	rm -f -v bwt/mkbwt bwt/mkfmi kaiju kaijux kaijup kaiju2krona mergeOutputs kaijuReport convertNR addTaxonNames
 	find . -name "*.o" -delete
 	$(MAKE) -C bwt/ clean
 
+uninstall:
+	rm -fv ../bin/*
+
 static: LDFLAGS = -static
 static: LDLIBS = $(LD_LIBS_STATIC)
 static: all
diff --git a/util/makeDB.sh b/util/makeDB.sh
index c09d820..aa6cb7e 100755
--- a/util/makeDB.sh
+++ b/util/makeDB.sh
@@ -12,6 +12,7 @@ db_refseq=0
 db_progenomes=0
 db_nr=0
 db_euk=0
+db_nr_all=0
 db_mar=0
 db_plasmids=0
 threadsBWT=5
@@ -37,6 +38,9 @@ echo
 echo  "$s" -n  NCBI BLAST non-redundant protein database \"nr\":
 echo  "$tab"   only Archaea, bacteria, and viruses
 echo
+echo  "$s" -N NCBI BLAST non-redundant protein database \"nr\":
+echo  "$tab"   all taxa
+echo
 echo  "$s" -e  NCBI BLAST non-redundant protein database \"nr\":
 echo  "$tab"   like -n, but additionally including fungi and microbial eukaryotes
 echo
@@ -87,6 +91,9 @@ while :; do
         -e|--euk)
             db_euk=1
             ;;
+        -N|--nra)
+            db_nr_all=1
+            ;;
         -v|--viruses)
             db_viruses=1
             ;;
@@ -115,7 +122,7 @@ while :; do
     shift
 done
 
-[ $db_plasmids -eq 1 -o $db_viruses -eq 1 -o $db_refseq -eq 1 -o $db_progenomes -eq 1 -o $db_nr -eq 1 -o $db_euk -eq 1 -o $db_mar -eq 1 ] || { echo "Error: Use one of the options -r, -p, -n, -v, -l, -m, or -e"; usage; exit 1; }
+[ $db_plasmids -eq 1 -o $db_viruses -eq 1 -o $db_refseq -eq 1 -o $db_progenomes -eq 1 -o $db_nr -eq 1 -o $db_euk -eq 1 -o $db_nr_all -eq 1 -o $db_mar -eq 1 ] || { echo "Error: Use one of the options -r, -p, -n, -v, -l, -m, or -e"; usage; exit 1; }
 
 #check if necessary programs are in the PATH
 command -v awk >/dev/null 2>/dev/null || { echo Error: awk not found; exit 1; }
@@ -188,7 +195,7 @@ then
 fi
 
 
-if [ $db_nr -eq 1 -o $db_euk -eq 1 ]
+if [ $db_nr -eq 1 -o $db_euk -eq 1 -o $db_nr_all -eq 1 ]
 then
 	if [ $DL -eq 1 ]
 	then
@@ -217,6 +224,22 @@ then
 		echo Kaiju only needs the files kaiju_db_nr_euk.fmi, nodes.dmp, and names.dmp.
 		echo The remaining files can be deleted.
 		echo
+	elif [ $db_nr_all -eq 1 ]
+	then
+		if [ $index_only -eq 0 ]
+		then
+			echo Converting NR file to Kaiju database
+			gunzip -c nr.gz | convertNR -t nodes.dmp -g prot.accession2taxid -a -o kaiju_db_nr_all.faa -A
+		fi
+		[ -r kaiju_db_nr_all.faa ] || { echo Missing file kaiju_db_nr_all.faa; exit 1; }
+		echo Creating BWT from Kaiju database
+		mkbwt -e $exponentSA_NR -n $threadsBWT -a ACDEFGHIKLMNPQRSTVWY -o kaiju_db_nr_all kaiju_db_nr_all.faa
+		echo Creating FM-index
+		mkfmi kaiju_db_nr_all
+		echo Done!
+		echo Kaiju only needs the files kaiju_db_nr_all.fmi, nodes.dmp, and names.dmp.
+		echo The remaining files can be deleted.
+		echo
 	else
 		if [ $index_only -eq 0 ]
 		then