diff --git a/api/api/api.go b/api/api/api.go
index 61c8833..86978ba 100644
--- a/api/api/api.go
+++ b/api/api/api.go
@@ -103,7 +103,17 @@ func InitializeApp() App {
 
 	// IO handlers.
 	app.Router.HandleFunc("/api/io/fasta/parse", appImpl.PostIoFastaParse)
+	app.Router.HandleFunc("/api/io/fasta/write", appImpl.PostIoFastaWrite)
 	app.Router.HandleFunc("/api/io/genbank/parse", appImpl.PostIoGenbankParse)
+	app.Router.HandleFunc("/api/io/genbank/write", appImpl.PostIoGenbankWrite)
+	app.Router.HandleFunc("/api/io/fastq/parse", appImpl.PostIoFastqParse)
+	app.Router.HandleFunc("/api/io/fastq/write", appImpl.PostIoFastqWrite)
+	app.Router.HandleFunc("/api/io/pileup/parse", appImpl.PostIoPileupParse)
+	app.Router.HandleFunc("/api/io/pileup/write", appImpl.PostIoPileupWrite)
+	app.Router.HandleFunc("/api/io/slow5/parse", appImpl.PostIoSlow5Parse)
+	app.Router.HandleFunc("/api/io/slow5/write", appImpl.PostIoSlow5Write)
+	app.Router.HandleFunc("/api/io/slow5/svb_compress", appImpl.PostIoSlow5SvbCompress)
+	app.Router.HandleFunc("/api/io/slow5/svb_decompress", appImpl.PostIoSlow5SvbDecompress)
 
 	// CDS design handlers.
 	app.Router.HandleFunc("/api/cds/fix", appImpl.PostCdsFix)
@@ -111,11 +121,51 @@ func InitializeApp() App {
 	app.Router.HandleFunc("/api/cds/translate", appImpl.PostCdsTranslate)
 
 	// PCR handlers.
+	app.Router.HandleFunc("/api/pcr/primers/debruijn_barcodes", appImpl.PostPcrPrimersDebruijnBarcodes)
+	app.Router.HandleFunc("/api/pcr/primers/marmur_doty", appImpl.PostPcrPrimersMarmurDoty)
+	app.Router.HandleFunc("/api/pcr/primers/santa_lucia", appImpl.PostPcrPrimersSantaLucia)
+	app.Router.HandleFunc("/api/pcr/primers/melting_temperature", appImpl.PostPcrPrimersMeltingTemperature)
+	app.Router.HandleFunc("/api/pcr/primers/design_primers", appImpl.PostPcrPrimersDesignPrimers)
 	app.Router.HandleFunc("/api/pcr/complex_pcr", appImpl.PostPcrComplexPcr)
 	app.Router.HandleFunc("/api/pcr/simple_pcr", appImpl.PostPcrSimplePcr)
 
-	// Synthesis handlers.
-	app.Router.HandleFunc("/api/synthesis/fragment", appImpl.PostCloningFragment)
+	// Cloning handlers.
+	app.Router.HandleFunc("/api/cloning/ligate", appImpl.PostCloningLigate)
+	app.Router.HandleFunc("/api/cloning/restriction_digest", appImpl.PostCloningRestrictionDigest)
+	app.Router.HandleFunc("/api/cloning/golden_gate", appImpl.PostCloningGoldenGate)
+	app.Router.HandleFunc("/api/cloning/fragment", appImpl.PostCloningFragment)
+
+	// Folding handlers.
+	app.Router.HandleFunc("/api/folding/zuker", appImpl.PostFoldingZuker)
+	app.Router.HandleFunc("/api/folding/linearfold/contra_fold_v2", appImpl.PostFoldingLinearfoldContraFoldV2)
+	app.Router.HandleFunc("/api/folding/linearfold/vienna_rna_fold", appImpl.PostFoldingLinearfoldViennaRnaFold)
+
+	// Seqhash handlers.
+	app.Router.HandleFunc("/api/seqhash", appImpl.PostSeqhash)
+	app.Router.HandleFunc("/api/seqhash_fragment", appImpl.PostSeqhashFragment)
+
+	// Codon Table handlers.
+	app.Router.HandleFunc("/api/codon_tables/new", appImpl.PostCodonTablesNew)
+	app.Router.HandleFunc("/api/codon_tables/from_genbank", appImpl.PostCodonTablesFromGenbank)
+	app.Router.HandleFunc("/api/codon_tables/compromise_tables", appImpl.PostCodonTablesCompromiseTables)
+	app.Router.HandleFunc("/api/codon_tables/add_tables", appImpl.PostCodonTablesAddTables)
+	app.Router.HandleFunc("/api/codon_tables/default_organisms", appImpl.GetCodonTablesDefaultOrganisms)
+	app.Router.HandleFunc("/api/codon_tables/get_organism_table", appImpl.PostCodonTablesGetOrganismTable)
+
+	// Alignment handlers.
+	app.Router.HandleFunc("/api/align/needleman_wunsch", appImpl.PostAlignNeedlemanWunsch)
+	app.Router.HandleFunc("/api/align/smith_waterman", appImpl.PostAlignSmithWaterman)
+	app.Router.HandleFunc("/api/align/mash", appImpl.PostAlignMash)
+	app.Router.HandleFunc("/api/align/mash_many", appImpl.PostAlignMashMany)
+
+	// Utils handlers.
+	app.Router.HandleFunc("/api/utils/reverse_complement", appImpl.PostUtilsReverseComplement)
+	app.Router.HandleFunc("/api/utils/is_palindromic", appImpl.PostUtilsIsPalindromic)
+
+	// Random handlers.
+	app.Router.HandleFunc("/api/random/random_dna", appImpl.PostRandomRandomDna)
+	app.Router.HandleFunc("/api/random/random_rna", appImpl.PostRandomRandomRna)
+	app.Router.HandleFunc("/api/random/random_protein", appImpl.PostRandomRandomProtein)
 
 	return app
 }
@@ -578,10 +628,10 @@ func (app *App) LuaPcrPrimersDesignPrimers(L *lua.LState) int { return 0 }
 *****************************************************************************
 */
 
-func (app *App) PostCloningGoldengate(ctx context.Context, request gen.PostCloningGoldengateRequestObject) (gen.PostCloningGoldengateResponseObject, error) {
+func (app *App) PostCloningGoldenGate(ctx context.Context, request gen.PostCloningGoldenGateRequestObject) (gen.PostCloningGoldenGateResponseObject, error) {
 	return nil, nil
 }
-func (app *App) LuaCloningGoldengate(L *lua.LState) int { return 0 }
+func (app *App) LuaCloningGoldenGate(L *lua.LState) int { return 0 }
 func (app *App) PostCloningLigate(ctx context.Context, request gen.PostCloningLigateRequestObject) (gen.PostCloningLigateResponseObject, error) {
 	return nil, nil
 }
@@ -626,7 +676,7 @@ func (app *App) LuaCloningFragment(L *lua.LState) int {
 		L.RaiseError(err.Error())
 		return 0
 	}
-	return app.luaResponse(L, "/api/synthesis/fragment", string(b))
+	return app.luaResponse(L, "/api/cloning/fragment", string(b))
 }
 
 /*
diff --git a/api/api/api_test.go b/api/api/api_test.go
index 293b90f..ff9ec92 100644
--- a/api/api/api_test.go
+++ b/api/api/api_test.go
@@ -141,7 +141,7 @@ func TestFragment(t *testing.T) {
 	if err != nil {
 		t.Errorf("Failed to marshal: %s", err)
 	}
-	req := httptest.NewRequest("POST", "/api/synthesis/fragment", bytes.NewBuffer(b))
+	req := httptest.NewRequest("POST", "/api/cloning/fragment", bytes.NewBuffer(b))
 	resp := httptest.NewRecorder()
 	app.Router.ServeHTTP(resp, req)
 
diff --git a/api/gen/dnadesign-server.gen.go b/api/gen/dnadesign-server.gen.go
index c1d5a62..2c949f8 100644
--- a/api/gen/dnadesign-server.gen.go
+++ b/api/gen/dnadesign-server.gen.go
@@ -48,8 +48,8 @@ type ServerInterface interface {
 	// (POST /cloning/fragment)
 	PostCloningFragment(w http.ResponseWriter, r *http.Request)
 	// Simulate GoldenGate assembly
-	// (POST /cloning/goldengate)
-	PostCloningGoldengate(w http.ResponseWriter, r *http.Request)
+	// (POST /cloning/golden_gate)
+	PostCloningGoldenGate(w http.ResponseWriter, r *http.Request)
 	// Simulate ligation
 	// (POST /cloning/ligate)
 	PostCloningLigate(w http.ResponseWriter, r *http.Request)
@@ -219,8 +219,8 @@ func (_ Unimplemented) PostCloningFragment(w http.ResponseWriter, r *http.Reques
 }
 
 // Simulate GoldenGate assembly
-// (POST /cloning/goldengate)
-func (_ Unimplemented) PostCloningGoldengate(w http.ResponseWriter, r *http.Request) {
+// (POST /cloning/golden_gate)
+func (_ Unimplemented) PostCloningGoldenGate(w http.ResponseWriter, r *http.Request) {
 	w.WriteHeader(http.StatusNotImplemented)
 }
 
@@ -581,12 +581,12 @@ func (siw *ServerInterfaceWrapper) PostCloningFragment(w http.ResponseWriter, r
 	handler.ServeHTTP(w, r.WithContext(ctx))
 }
 
-// PostCloningGoldengate operation middleware
-func (siw *ServerInterfaceWrapper) PostCloningGoldengate(w http.ResponseWriter, r *http.Request) {
+// PostCloningGoldenGate operation middleware
+func (siw *ServerInterfaceWrapper) PostCloningGoldenGate(w http.ResponseWriter, r *http.Request) {
 	ctx := r.Context()
 
 	handler := http.Handler(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-		siw.Handler.PostCloningGoldengate(w, r)
+		siw.Handler.PostCloningGoldenGate(w, r)
 	}))
 
 	for _, middleware := range siw.HandlerMiddlewares {
@@ -1304,7 +1304,7 @@ func HandlerWithOptions(si ServerInterface, options ChiServerOptions) http.Handl
 		r.Post(options.BaseURL+"/cloning/fragment", wrapper.PostCloningFragment)
 	})
 	r.Group(func(r chi.Router) {
-		r.Post(options.BaseURL+"/cloning/goldengate", wrapper.PostCloningGoldengate)
+		r.Post(options.BaseURL+"/cloning/golden_gate", wrapper.PostCloningGoldenGate)
 	})
 	r.Group(func(r chi.Router) {
 		r.Post(options.BaseURL+"/cloning/ligate", wrapper.PostCloningLigate)
@@ -1636,25 +1636,25 @@ func (response PostCloningFragment500TextResponse) VisitPostCloningFragmentRespo
 	return err
 }
 
-type PostCloningGoldengateRequestObject struct {
-	Body *PostCloningGoldengateJSONRequestBody
+type PostCloningGoldenGateRequestObject struct {
+	Body *PostCloningGoldenGateJSONRequestBody
 }
 
-type PostCloningGoldengateResponseObject interface {
-	VisitPostCloningGoldengateResponse(w http.ResponseWriter) error
+type PostCloningGoldenGateResponseObject interface {
+	VisitPostCloningGoldenGateResponse(w http.ResponseWriter) error
 }
 
-type PostCloningGoldengate200Response struct {
+type PostCloningGoldenGate200Response struct {
 }
 
-func (response PostCloningGoldengate200Response) VisitPostCloningGoldengateResponse(w http.ResponseWriter) error {
+func (response PostCloningGoldenGate200Response) VisitPostCloningGoldenGateResponse(w http.ResponseWriter) error {
 	w.WriteHeader(200)
 	return nil
 }
 
-type PostCloningGoldengate500TextResponse string
+type PostCloningGoldenGate500TextResponse string
 
-func (response PostCloningGoldengate500TextResponse) VisitPostCloningGoldengateResponse(w http.ResponseWriter) error {
+func (response PostCloningGoldenGate500TextResponse) VisitPostCloningGoldenGateResponse(w http.ResponseWriter) error {
 	w.Header().Set("Content-Type", "text/plain")
 	w.WriteHeader(500)
 
@@ -2426,8 +2426,8 @@ type StrictServerInterface interface {
 	// (POST /cloning/fragment)
 	PostCloningFragment(ctx context.Context, request PostCloningFragmentRequestObject) (PostCloningFragmentResponseObject, error)
 	// Simulate GoldenGate assembly
-	// (POST /cloning/goldengate)
-	PostCloningGoldengate(ctx context.Context, request PostCloningGoldengateRequestObject) (PostCloningGoldengateResponseObject, error)
+	// (POST /cloning/golden_gate)
+	PostCloningGoldenGate(ctx context.Context, request PostCloningGoldenGateRequestObject) (PostCloningGoldenGateResponseObject, error)
 	// Simulate ligation
 	// (POST /cloning/ligate)
 	PostCloningLigate(ctx context.Context, request PostCloningLigateRequestObject) (PostCloningLigateResponseObject, error)
@@ -2821,11 +2821,11 @@ func (sh *strictHandler) PostCloningFragment(w http.ResponseWriter, r *http.Requ
 	}
 }
 
-// PostCloningGoldengate operation middleware
-func (sh *strictHandler) PostCloningGoldengate(w http.ResponseWriter, r *http.Request) {
-	var request PostCloningGoldengateRequestObject
+// PostCloningGoldenGate operation middleware
+func (sh *strictHandler) PostCloningGoldenGate(w http.ResponseWriter, r *http.Request) {
+	var request PostCloningGoldenGateRequestObject
 
-	var body PostCloningGoldengateJSONRequestBody
+	var body PostCloningGoldenGateJSONRequestBody
 	if err := json.NewDecoder(r.Body).Decode(&body); err != nil {
 		sh.options.RequestErrorHandlerFunc(w, r, fmt.Errorf("can't decode JSON body: %w", err))
 		return
@@ -2833,18 +2833,18 @@ func (sh *strictHandler) PostCloningGoldengate(w http.ResponseWriter, r *http.Re
 	request.Body = &body
 
 	handler := func(ctx context.Context, w http.ResponseWriter, r *http.Request, request interface{}) (interface{}, error) {
-		return sh.ssi.PostCloningGoldengate(ctx, request.(PostCloningGoldengateRequestObject))
+		return sh.ssi.PostCloningGoldenGate(ctx, request.(PostCloningGoldenGateRequestObject))
 	}
 	for _, middleware := range sh.middlewares {
-		handler = middleware(handler, "PostCloningGoldengate")
+		handler = middleware(handler, "PostCloningGoldenGate")
 	}
 
 	response, err := handler(r.Context(), w, r, request)
 
 	if err != nil {
 		sh.options.ResponseErrorHandlerFunc(w, r, err)
-	} else if validResponse, ok := response.(PostCloningGoldengateResponseObject); ok {
-		if err := validResponse.VisitPostCloningGoldengateResponse(w); err != nil {
+	} else if validResponse, ok := response.(PostCloningGoldenGateResponseObject); ok {
+		if err := validResponse.VisitPostCloningGoldenGateResponse(w); err != nil {
 			sh.options.ResponseErrorHandlerFunc(w, r, err)
 		}
 	} else if response != nil {
@@ -4029,75 +4029,75 @@ func (sh *strictHandler) PostUtilsReverseComplement(w http.ResponseWriter, r *ht
 // Base64 encoded, gzipped, json marshaled Swagger object
 var swaggerSpec = []string{
 
-	"H4sIAAAAAAAC/+xdbXPbtpP/KhjevVQjN73e9e93thy7nrEdVfI/nbmbjAYiVxJqEmAA0A/t5LvfACBI",
-	"kAJJyJYf0uZNIpm7i8XubxcLEID+imKW5YwClSI6/CsS8QYyrD8eZYSyo5gk6kvOWQ5cEtCPJixhVH8i",
-	"EjL94T85rKLD6D/GtbxxKWysyaOvo0g+5BAdRphz/KC+X4CUwBV7+URITug6+vp1FHH4UhAOSXT4f5Zu",
-	"ZBv+XIliyz8glkrWkZQ43mRA5ba+MaOyfNBqaBRRnMGwBppqVAnyKXCMBUxY4Wt/iQV4G48tffmEUAlr",
-	"4FvNawGW3Nf4ZIPpGrZbPuUs87Y8ZYJIwqiv8VE0Aywaz2rGuYTcz3TNhu1YNVsKGhkNNXPVrLeDGkNb",
-	"/bvmJE/B79nfgaw3Ida1QiqWTgWu8TL1WLkKlfCYqKPLExdzibn0BNlWF7cZWb47X8scbusNkSO3oz4b",
-	"faB/PphoAlpkStaxwOfRKDpeCvXfFH+Z6K8iOz53JNSKnWIh8Qxixj1phyRAJVkRb8oYRQK+FEDjgGh2",
-	"BDlsvh4pfb7MAHu0Oe/X5mOucI5TTYuThJiv04aMLsfUCvxW4JTIB38oBnf43O1wxVZL93YdsCy4B+1Y",
-	"Sk6WhYTeroWDdqvlBETMSd5KT7WAlMXYPuyLsQtL1w8Oq8GQEfXTpnYj1xhOI46OXtNyvPaPVKeM32Ge",
-	"fLwFrjK6V9sZ3AIX0EsTDo15H/zPgC4xvekKyJWBSHjWs5jyoCADiYfYLxXNTpGupY5qRQfC/VfACfBP",
-	"OC18WT4I98Mh/YEmZqAzrV3iPECeM85uCVT56YyzIj8/8XPMU3b38yfgwh9RPpkXToy1i6ksTyFr1lNL",
-	"xlLAOtKAJn4tVuQWppxkMMVcEpz62dfLG9v23OjnM+ofjFA/v1Cjl18BUSyt6HDIuklkK3NtOAx2qYVI",
-	"o58x08g1Ztkpj518DfkM1erhZ79bC+HxKeFxkWLe4RKTBU7ILRFdOTljCVkR0/QJltBBlEJcpHDtz7ed",
-	"xXgdtROWdEHCklwAXctNcEnfYmspud15T1e31BvVBvU54bJMda1hNY5BdNp36c4ugoBbz0c8yE26XJTA",
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-	"pURNGMy3HAvJOBHeKcOUpFDkF4R6huz+WW5fba3G1EnX7Nw8noEoUrljsVvB5bhrTeARpdvInVc3W3B7",
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-	"p9e2F0Bn+G5O1k3YOCyXkBBMj2HFOHh1/bhaicYSUf1o1gKW+8RptB3e2wo78T1QiyuCxrNmztlyilvG",
-	"4yxPCV3PmoN3rbReubks7jvY1dNr0hh13SWxlu3VnwhdmUU9E0vRydURSkCQNUVH03NnGDmMDt4dvPtR",
-	"D8M5UJyT6DD66d3BuwMVRlhutPnGOCVrOs6w0PVZzoR2i4KEhtp5Eh2qVCaPFN2lIjPBCkIes+ShtZaL",
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-	"CgTRZ8XmAGeRYfoQiJ5LRbovBKmkjDkRjC6s03Yc+wMxuEeIlTPMLbVfF2pti9UJrDWsbeHqggiJ2Ao1",
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-	"Z3+wrh3ET5yI8Yrcu5BpqnBK7kGgmGUZoyjnbJlCJhChaHIy1//nHHJsMIZWjCNVwYkHKjcgiHgXjTwQ",
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-	"JQpdyMg1kE/LcdlK+jqK/mvLIhLu5ThPMWnZoq3nVpv/FsARoXkhEXDOdKXw8/7En1MJasKPBPBb4LaN",
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-	"DIRpgjBapQzL1ygKSj10Ua2K6zOWJkDPTLKsIstESCu61pp0PZyBDf1ZTb63CKs26/XVA+WWPgfou3o/",
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-	"h+OpYb+ouCeaWf350/uXeCvRtY77CtvymFwsOY5vOo48P2U3Q2lmu5ehnXC0zZEiQtrq1s2lc7tdfUuA",
-	"Urzg1Lh7R19/0twzqt39Qq+gINN6lYdf67cG/zPy2PUfjwzjITS7OkKlj/qh8WdxU+6KH0LB/2rK7z5/",
-	"ez7XnkElTafHCRuvsJB4nGMuBuYC50wf/Z9qyj6XBw9ne9ul2ruE7txXEDCz191L0OnR/PoIcc32Gqu4",
-	"Wo1SiwTrE9LWg4S1nXfHiQxz3u+a8rlfWvRbPGgp3fR8RVJAqncSKBJVMZU+tKyluxVmrS/hUP/yLULd",
-	"XIWxG9B/q4HeAcLfhs0aDMIvLwbCTlsEQ/C3R0Cw11bl0lUYCMtlnm8Nhq3Fu2Ao2lWt1866Vo8ANwaB",
-	"vpT3IrAftH3Yq/3SAruBP8BuuT4JHIZ+c2p4GPw71WNY4qCT2fhlj9n0udQ5PR0QS9U7aMOGFJ8/r5cE",
-	"J4PeCgK5kfZUjLfWa7Tue7HTy1f+nUgbLOxLxygJyOFrh9uw/0TK7n4OCzZ9FvlvHWtN5TbVye8+SLmH",
-	"xHX7eIf74+rj3YFw9A6K2ocmpfqC2DwexIC4XS70C3sQIggK89vlxNLvCxD8UQe230zojqIMi5tHxrQ1",
-	"JiSI4zskjB3aC3iGBs3wHTKWMmc35p+OB72bwK7+Pak5njnkR1E6eEfATrZ9Tu/vE6VNDNQG70NBTbUz",
-	"DoIGau3+/Y7TbzGZvtGxvU7n4XV1f47PYz42d5TdL/J4YNl2GvOJoZ3G+1u37b+bLOckA77rjZOYr0Eu",
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 }
 
 // GetSwagger returns the content of the embedded swagger specification file
diff --git a/api/gen/dnadesign-types.gen.go b/api/gen/dnadesign-types.gen.go
index b6757a9..f6ba8b1 100644
--- a/api/gen/dnadesign-types.gen.go
+++ b/api/gen/dnadesign-types.gen.go
@@ -257,8 +257,8 @@ type PostCloningFragmentJSONBody struct {
 	Sequence         string    `json:"sequence"`
 }
 
-// PostCloningGoldengateJSONBody defines parameters for PostCloningGoldengate.
-type PostCloningGoldengateJSONBody struct {
+// PostCloningGoldenGateJSONBody defines parameters for PostCloningGoldenGate.
+type PostCloningGoldenGateJSONBody struct {
 	Enzyme    *Enzyme   `json:"enzyme,omitempty"`
 	Sequences *[]string `json:"sequences,omitempty"`
 }
@@ -498,8 +498,8 @@ type PostCdsTranslateJSONRequestBody PostCdsTranslateJSONBody
 // PostCloningFragmentJSONRequestBody defines body for PostCloningFragment for application/json ContentType.
 type PostCloningFragmentJSONRequestBody PostCloningFragmentJSONBody
 
-// PostCloningGoldengateJSONRequestBody defines body for PostCloningGoldengate for application/json ContentType.
-type PostCloningGoldengateJSONRequestBody PostCloningGoldengateJSONBody
+// PostCloningGoldenGateJSONRequestBody defines body for PostCloningGoldenGate for application/json ContentType.
+type PostCloningGoldenGateJSONRequestBody PostCloningGoldenGateJSONBody
 
 // PostCloningLigateJSONRequestBody defines body for PostCloningLigate for application/json ContentType.
 type PostCloningLigateJSONRequestBody = PostCloningLigateJSONBody
diff --git a/api/spec.yaml b/api/spec.yaml
index 3e8db23..1e490c1 100644
--- a/api/spec.yaml
+++ b/api/spec.yaml
@@ -1107,7 +1107,7 @@ paths:
             text/plain:
               schema:
                 type: string
-  /cloning/goldengate:
+  /cloning/golden_gate:
     post:
       tags:
         - cloning