--- a/src/lambda.cpp
+++ b/src/lambda.cpp
@@ -33,7 +33,7 @@
 #include "holders.hpp"
 #include "lambda.hpp"
 
-using namespace seqan;
+using namespace seqan2;
 
 // inline BlastFormatFile
 // _fileType(LambdaOptions const & options)
@@ -116,15 +116,15 @@
 int main(int argc, char const ** argv)
 {
     // Parse the command line.
-    seqan::ArgumentParser parser;
+    seqan2::ArgumentParser parser;
     LambdaOptions options;
-    seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
+    seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
 
     // If there was an error parsing or built-in argument parser functionality
     // was triggered then we exit the program.  The return code is 1 if there
     // were errors and 0 if there were none.
-    if (res != seqan::ArgumentParser::PARSE_OK)
-        return res == seqan::ArgumentParser::PARSE_ERROR;
+    if (res != seqan2::ArgumentParser::PARSE_OK)
+        return res == seqan2::ArgumentParser::PARSE_ERROR;
 
     if (std::string(CMAKE_BUILD_TYPE) != "Release")
         std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
--- a/src/lambda.hpp
+++ b/src/lambda.hpp
@@ -42,7 +42,7 @@
 #include "match.hpp"
 #include "misc.hpp"
 
-using namespace seqan;
+using namespace seqan2;
 
 // ============================================================================
 // Forwards
--- a/src/lambda_indexer.cpp
+++ b/src/lambda_indexer.cpp
@@ -30,7 +30,7 @@
 
 #include "lambda_indexer.hpp"
 
-using namespace seqan;
+using namespace seqan2;
 
 // ==========================================================================
 // Forwards
@@ -72,15 +72,15 @@
 int main(int argc, char const ** argv)
 {
     // Parse the command line.
-    seqan::ArgumentParser parser;
+    seqan2::ArgumentParser parser;
     LambdaIndexerOptions options;
-    seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
+    seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
 
     // If there was an error parsing or built-in argument parser functionality
     // was triggered then we exit the program.  The return code is 1 if there
     // were errors and 0 if there were none.
-    if (res != seqan::ArgumentParser::PARSE_OK)
-        return res == seqan::ArgumentParser::PARSE_ERROR;
+    if (res != seqan2::ArgumentParser::PARSE_OK)
+        return res == seqan2::ArgumentParser::PARSE_ERROR;
 
     if (std::string(CMAKE_BUILD_TYPE) != "Release")
         std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
--- a/src/lambda_indexer.hpp
+++ b/src/lambda_indexer.hpp
@@ -37,7 +37,7 @@
 #include "radix_inplace.h"
 #include "lambda_indexer_misc.hpp"
 
-using namespace seqan;
+using namespace seqan2;
 
 // --------------------------------------------------------------------------
 // Function loadSubj()
--- a/src/match.hpp
+++ b/src/match.hpp
@@ -28,7 +28,7 @@
 
 #include "options.hpp"
 
-using namespace seqan;
+using namespace seqan2;
 
 //-----------------------------------------------------------------------------
 //                  Finder
--- a/src/misc.hpp
+++ b/src/misc.hpp
@@ -33,7 +33,7 @@
 
 #include "options.hpp"
 
-using namespace seqan;
+using namespace seqan2;
 
 // ============================================================================
 // Forwards
@@ -78,8 +78,8 @@
 inline std::basic_ostream<char> &
 operator<<(std::basic_ostream<char> & out,
            const Iter<const String<SimpleType<unsigned char,TAlph>,
-                                    seqan::Packed<> >,
-                      seqan::Packed<> > it)
+                                    seqan2::Packed<> >,
+                      seqan2::Packed<> > it)
 {
     out << *it;
     return out;
--- a/src/options.hpp
+++ b/src/options.hpp
@@ -111,7 +111,7 @@
 
 }
 
-using namespace seqan;
+using namespace seqan2;
 
 // Index Specs
 struct LambdaFMIndexConfig
--- a/src/output.hpp
+++ b/src/output.hpp
@@ -25,7 +25,7 @@
 #include <seqan/blast.h>
 #include <seqan/bam_io.h>
 
-using namespace seqan;
+using namespace seqan2;
 
 template <typename TVoidSpec = void>
 struct SamBamExtraTags
@@ -313,7 +313,7 @@
     } else // SAM or BAM
     {
         open(globalHolder.outfileBam, toCString(options.output));
-        auto & context          = seqan::context(globalHolder.outfileBam);
+        auto & context          = seqan2::context(globalHolder.outfileBam);
         auto & subjSeqLengths   = contigLengths(context);
         auto & subjIds          = contigNames(context);
 
@@ -407,7 +407,7 @@
         {
             // we only write the header records that we actually created ourselves
             for (unsigned i = 0; i < length(header); ++i)
-                write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
+                write(globalHolder.outfileBam.iter, header[i], seqan2::context(globalHolder.outfileBam), Sam());
         }
         else
         {