diff --git a/README.md b/README.md
index b8c68ee..823f49a 100644
--- a/README.md
+++ b/README.md
@@ -129,7 +129,7 @@ The code will not work with perl 5.8 or below (pre-modern perl). We no longer te
 * cdhit 4.6.1
 * ncbi blast+ 2.4.0
 * mcl 14-137
-* bedtools 2.26.0
+* bedtools 2.27.1
 * prank 130410
 * GNU parallel 20130922, 20160722, 20150122
 * FastTree 2.1.9
diff --git a/dist.ini b/dist.ini
index e673cd7..17fdd3b 100644
--- a/dist.ini
+++ b/dist.ini
@@ -3,7 +3,7 @@ author  = Andrew J. Page <ap13@sanger.ac.uk>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
 copyright_year   = 2013
-version = 3.11.0
+version = 3.11.1
 main_module = lib/Bio/Roary.pm
 
 [MetaResources]
diff --git a/install_dependencies.sh b/install_dependencies.sh
index 253ed7b..bdc0256 100755
--- a/install_dependencies.sh
+++ b/install_dependencies.sh
@@ -11,7 +11,7 @@ PARALLEL_VERSION=${PARALLEL_VERSION:-"20160722"}
 PARALLEL_DOWNLOAD_FILENAME="parallel-${PARALLEL_VERSION}.tar.bz2" 
 PARALLEL_URL="http://ftp.gnu.org/gnu/parallel/${PARALLEL_DOWNLOAD_FILENAME}"
 
-BEDTOOLS_VERSION="2.26.0"
+BEDTOOLS_VERSION="2.27.1"
 BEDTOOLS_DOWNLOAD_FILENAME="bedtools-${BEDTOOLS_VERSION}.tar.gz"
 BEDTOOLS_URL="https://github.com/arq5x/bedtools2/releases/download/v${BEDTOOLS_VERSION}/${BEDTOOLS_DOWNLOAD_FILENAME}"
 
diff --git a/lib/Bio/Roary/ExtractProteomeFromGFF.pm b/lib/Bio/Roary/ExtractProteomeFromGFF.pm
index 8940aed..a96e087 100644
--- a/lib/Bio/Roary/ExtractProteomeFromGFF.pm
+++ b/lib/Bio/Roary/ExtractProteomeFromGFF.pm
@@ -132,8 +132,13 @@ sub _cleanup_fasta {
     open( my $in,  '<', $infile );
     open( my $out, '>', $outfile );
     while ( my $line = <$in> ) {
-        chomp $line;
-        $line =~ s/"//g if ( $line =~ /^>/ );
+       chomp $line;
+       if ( $line =~ /^>/ )
+	   {
+	   	 $line =~ s/"//g;
+		 # newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them
+		 $line =~ s!\([-+]\)!!;
+	   }
 	
 	if($line =~ /^(>[^:]+)/)
 	{
diff --git a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
index 14413dc..2a16b1a 100644
--- a/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
+++ b/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
@@ -177,7 +177,12 @@ sub _cleanup_fasta {
     open( my $out, '>', $outfile );
     while ( my $line = <$in> ) {
         chomp $line;
-        $line =~ s/"//g if ( $line =~ /^>/ );
+        if ( $line =~ /^>/ )
+		{
+			$line =~ s/"//g ;
+			# newer versions of Bedtools add (-) or (+) to the end of the sequence name, remove them
+			$line =~ s!\([-+]\)!!;
+		}
 	
 	if($line =~ /^(>[^:]+)/)
 	{