diff --git a/scripts/Makefile b/scripts/Makefile
index 78a44bf..dc2d432 100755
--- a/scripts/Makefile
+++ b/scripts/Makefile
@@ -16,20 +16,21 @@ trimmomatic:
 	rm Trimmomatic-0.32.zip
 	mv Trimmomatic-0.32/ plugins/
 Pfam:
-	wget http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz
-	tar -zxf hmmer-3.1b1-linux-intel-x86_64.tar.gz
-	cd hmmer-3.1b1-linux-intel-x86_64 && ./configure && $(MAKE) -j6 && $(MAKE) -j6 check
-	cp hmmer-3.1b1-linux-intel-x86_64/src/hmmpress .
-	cp hmmer-3.1b1-linux-intel-x86_64/src/hmmscan .
-	cp hmmer-3.1b1-linux-intel-x86_64/src/hmmsearch .
-	cp hmmer-3.1b1-linux-intel-x86_64/src/hmmstat .	
+	wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
+	tar -zxf hmmer-3.1b2-linux-intel-x86_64.tar.gz
+	cd hmmer-3.1b2-linux-intel-x86_64 && ./configure && $(MAKE) -j6 && $(MAKE) -j6 check
+	cp hmmer-3.1b2-linux-intel-x86_64/src/hmmpress .
+	cp hmmer-3.1b2-linux-intel-x86_64/src/hmmscan .
+	cp hmmer-3.1b2-linux-intel-x86_64/src/hmmsearch .
+	cp hmmer-3.1b2-linux-intel-x86_64/src/hmmstat .	
+	#The file bellow was not found in the url bellow, could you provide this file?
 	wget http://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin	
 	hmmpress Pfam-AB.hmm.bin
 GRCm38:
 	wget ftp://ftp.ensembl.org/pub/release-71/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.71.cdna.all.fa.gz
 	gzip -d Mus_musculus.GRCm38.71.cdna.all.fa.gz
 clean:
-	rm trimmomatic-0.32.jar express hmmer-3.1b1-linux-intel-x86_64.tar.gz Pfam-A.hmm* Mus_musculus.GRCm38.71.cdna.all.fa
-	rm -fr plugins/* hmmer-3.1b1-linux-intel-x86_64
+	rm trimmomatic-0.32.jar express hmmer-3.1b2-linux-intel-x86_64.tar.gz Pfam-A.hmm* Mus_musculus.GRCm38.71.cdna.all.fa
+	rm -fr plugins/* hmmer-3.1b2-linux-intel-x86_64
 clean_check:
-	rm -fr unit_test/*
\ No newline at end of file
+	rm -fr unit_test/*