merge-update from trunk

diff --combined .gitattributes
index 1f8c325ff4b9e402f4f318c596dcefc2b5b33320,e6bb9df13a99bf906f9bb0b0bf78c8ce9ee2a42f..18d46484697e899bc3d71385e7d2af7e4f6b7a74
--- 1/.gitattributes
--- 2/.gitattributes
+++ b/.gitattributes
@@@ -369,16 -369,7 +369,16 @@@ eu.etaxonomy.taxeditor.editor/icons/edi
  eu.etaxonomy.taxeditor.editor/icons/emblem-photos.png -text
  eu.etaxonomy.taxeditor.editor/icons/leaf_detail.png -text
  eu.etaxonomy.taxeditor.editor/icons/link_obj.gif -text
 +eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-left-16x16.png -text
 +eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-left-disabled-16x16.png -text
 +eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-16x16.png -text
 +eu.etaxonomy.taxeditor.editor/icons/pherogram-insert-right-disabled-16x16.png -text
  eu.etaxonomy.taxeditor.editor/icons/xper64.png -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-alignment-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/biojava3-core-3.0.7.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/commons-lang3-3.1.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/core-1.8.5.jar -text
 +eu.etaxonomy.taxeditor.editor/lib/sequencing-1.8.5.jar -text
  eu.etaxonomy.taxeditor.editor/p2.inf -text
  eu.etaxonomy.taxeditor.editor/plugin.xml -text
  eu.etaxonomy.taxeditor.editor/pom.xml -text
@@@ -404,23 -395,13 +404,23 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/CdmAuthorityEditorInput.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/group/authority/handler/EditCdmAuthoritiesHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditNewTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/EditSequenceHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/LoadPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenAlignmentEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenChecklistEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenDerivateViewHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenParentHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/OpenTaxonEditorHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveAllHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SaveTaxonHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/ShowPherogramHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/SpecimenPropertyTester.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/TaxonParameterConverter.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/CreateConsensusSequenceHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ReverseComplementHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleInsertOverwriteHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/ToggleLeftRightInsertionHandler.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/alignmenteditor/UpdateConsensusSequenceHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewNameHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewPersonHandler.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/handler/create/NewReferenceHandler.java -text
@@@ -448,12 -429,6 +448,12 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/CreateNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/DeleteNodeOperation.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/key/polytomous/operation/RefreshNodeNumberingOperation.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditor.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/AlignmentEditorInput.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/CDMAlignmentObjectPlaceholder.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/ContigSequenceDataProvider.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramMouseListener.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/molecular/PherogramViewPart.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/TaxonNameEditor.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroup.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/name/container/AbstractGroupedContainer.java -text
@@@ -643,10 -618,7 +643,10 @@@ eu.etaxonomy.taxeditor.editor/src/main/
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidationProblemsView.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorClassMarkerField.java -text
  eu.etaxonomy.taxeditor.editor/src/main/java/eu/etaxonomy/taxeditor/editor/view/validation/ValidatorMessageMarkerField.java -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR430_JR-P01.ab1 -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/AlignmentTestData/JR444_JR-P05.ab1 -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/TaonDescriptionEditor.screen -text
 +eu.etaxonomy.taxeditor.editor/src/main/resources/TestPherogram_qualityScore.scf -text
  eu.etaxonomy.taxeditor.editor/src/main/resources/log4j.properties -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/Application.java -text
  eu.etaxonomy.taxeditor.editor/src/test/java/eu/etaxonomy/taxeditor/editor/ApplicationActionBarAdvisor.java -text
@@@ -977,6 -949,7 +977,7 @@@ eu.etaxonomy.taxeditor.navigation/icons
  eu.etaxonomy.taxeditor.navigation/p2.inf -text
  eu.etaxonomy.taxeditor.navigation/plugin.xml -text
  eu.etaxonomy.taxeditor.navigation/pom.xml -text
+ eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigationCdmViewer.java -text
  eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigationUtil.java -text
  eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/NavigatorStateManager.java -text
  eu.etaxonomy.taxeditor.navigation/src/main/java/eu/etaxonomy/taxeditor/navigation/RecentNamesContributionItem.java -text
@@@ -1289,6 -1262,7 +1290,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/featuretree/SelectFeatureTreeWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/featuretree/SelectFeatureTreeWizardPage.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/OpenDistributionEditorWizardHandler.java -text
+ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/OpenHandler.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/OpenPasswordWizzardHandler.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/handler/ShowLoginWindowHandler.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/identificationkey/AbstractIdentificaitonKeyWizard.java -text
@@@ -1363,6 -1337,7 +1365,7 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AbstractNewEntityWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/AmplificationGeneralWizardPage.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/ExternalReferenceServiceWizardPage.java -text
+ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/IWizardPageListener.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewAmplificationWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewClassificationWizard.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/newWizard/NewCollectionWizard.java -text
@@@ -1608,7 -1583,6 +1611,6 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/ScopeSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StateDataElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StateDataSection.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StateModifierElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StatisticalMeasurementValueElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/StatisticalMeasurementValueSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/description/detail/AbstractDetailedDescriptionDetailElement.java -text
@@@ -1800,7 -1774,8 +1802,8 @@@ eu.etaxonomy.taxeditor.store/src/main/j
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/NamedAreaDetailElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/NamedAreaDetailSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/NamedAreaLevelDetailSection.java -text
- eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StateModifierCollectionSection.java -text
+ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/RecommendedModifierVocabulariesCollectionSection.java -text
+ eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/RecommendedModifierVocabulariesElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StateVocabularyCollectionElement.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StateVocabularyCollectionSection.java -text
  eu.etaxonomy.taxeditor.store/src/main/java/eu/etaxonomy/taxeditor/ui/section/vocabulary/StatisticalMeasureCollectionElement.java -text

diff --combined .gitignore
index 5c8b928b8e9810e6ba3615b0efdeead665c5c54d,5c8b928b8e9810e6ba3615b0efdeead665c5c54d..074683469e08c4a0d5b4632b9a11b4499d953467
--- 1/.gitignore
--- 2/.gitignore
+++ b/.gitignore
@@@ -5,14 -5,14 +5,43 @@@ eu.etaxonomy.taxeditor.bulkeditor/.sett
  eu.etaxonomy.taxeditor.bulkeditor/target
  eu.etaxonomy.taxeditor.cdmlib/.directory
  eu.etaxonomy.taxeditor.cdmlib/.settings
++eu.etaxonomy.taxeditor.cdmlib/META-INF/bin
++eu.etaxonomy.taxeditor.cdmlib/bin
  eu.etaxonomy.taxeditor.cdmlib/cdmlib-*.jar
  eu.etaxonomy.taxeditor.cdmlib/cdmlib-*.zip
  eu.etaxonomy.taxeditor.cdmlib/dist
++eu.etaxonomy.taxeditor.cdmlib/lib/bin
  eu.etaxonomy.taxeditor.cdmlib/lib/cdmlib*
  eu.etaxonomy.taxeditor.cdmlib/lib/org.eclipse.equinox.servletbridge.extensionbundle-1.2.0.v20100503.jar
  eu.etaxonomy.taxeditor.cdmlib/lib/org.eclipse.equinox.transforms.hook-1.0.300.v20100719.jar
  eu.etaxonomy.taxeditor.cdmlib/lib/org.eclipse.equinox.weaving.hook-1.0.100.v20110502.jar
  eu.etaxonomy.taxeditor.cdmlib/log4j-1.2.14src.zip
++eu.etaxonomy.taxeditor.cdmlib/src/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/cdm/api/application/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/cdm/api/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/cdm/api/cache/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/cdm/api/lazyloading/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/cdm/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/eu/etaxonomy/cdm/remote/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/org/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/org/hibernate/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/org/hibernate/collection/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/org/hibernate/collection/internal/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/java/org/hibernate/proxy/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/resources/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/etaxonomy/bin
++eu.etaxonomy.taxeditor.cdmlib/src/main/resources/eu/etaxonomy/cdm/bin
++eu.etaxonomy.taxeditor.cdmlib/src/test/bin
++eu.etaxonomy.taxeditor.cdmlib/src/test/resources/bin
++eu.etaxonomy.taxeditor.cdmlib/src/test/resources/eu/bin
++eu.etaxonomy.taxeditor.cdmlib/src/test/resources/eu/etaxonomy/bin
++eu.etaxonomy.taxeditor.cdmlib/src/test/resources/eu/etaxonomy/cdm/bin
++eu.etaxonomy.taxeditor.cdmlib/src/test/resources/eu/etaxonomy/cdm/datasources/bin
  eu.etaxonomy.taxeditor.cdmlib/target
  eu.etaxonomy.taxeditor.editor/.settings
  eu.etaxonomy.taxeditor.editor/target

diff --combined eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
index a1f584654a8e6045c67fb8596890414f5d357434,a455f7ddba87a2e5fc6e09f8cca4dcb8fa36617d..3a8274a3d5c918bbb978933d67e17c2757c4db20
--- 1/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
--- 2/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.cdmlib/META-INF/MANIFEST.MF
@@@ -2,7 -2,7 +2,7 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: CDM Library Dependencies Plugin
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.cdmlib;singleton:=true
- Bundle-Version: 3.5.2.qualifier
+ Bundle-Version: 3.6.1.qualifier
  Eclipse-BundleShape: dir
  Export-Package: com.google.api,
   com.google.api.detect,
@@@ -195,6 -195,7 +195,7 @@@
   org.apache.commons.collections;uses:="org.apache.commons.collections.keyvalue,new org.apache.commons.collections",
   org.apache.commons.io;uses:="org.apache.commons.io.filefilter",
   org.apache.commons.lang;uses:="org.apache.commons.lang.exception",
+  org.apache.commons.lang.exception,
   org.apache.fop.apps,
   org.apache.http,
   org.apache.http.client,
@@@ -257,6 -258,7 +258,6 @@@
   org.apache.lucene.util,
   org.apache.sanselan;uses:="org.apache.sanselan.common,org.apache.sanselan.common.byteSources",
   org.apache.xerces.dom,
 - org.eclipse.osgi.internal.loader,
   org.eclipse.osgi.util,
   org.h2.jdbc,
   org.hamcrest,
@@@ -301,6 -303,7 +302,6 @@@
   org.joda.time.format;uses:="org.joda.time",
   org.joda.time.tz;uses:="org.joda.time",
   org.junit;uses:="org.hamcrest",
 - org.junit.runner,
   org.odftoolkit.odfdom,
   org.odftoolkit.odfdom.doc,
   org.odftoolkit.odfdom.doc.office,
@@@ -604,22 -607,22 +605,22 @@@ Bundle-ClassPath: .
   lib/spring-security-remoting-3.1.3.RELEASE.jar,
   lib/jena-core-2.11.2.jar,
   lib/jena-iri-1.0.2.jar,
-  lib/cdmlib-commons-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-commons-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-ext-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-ext-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-io-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-io-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-model-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-model-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-persistence-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-persistence-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-print-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-print-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-remote-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-remote-3.5.2-SNAPSHOT.jar,
-  lib/cdmlib-services-3.5.2-SNAPSHOT-sources.jar,
-  lib/cdmlib-services-3.5.2-SNAPSHOT.jar,
+  lib/cdmlib-commons-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-commons-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-ext-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-ext-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-io-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-io-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-model-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-model-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-persistence-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-persistence-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-print-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-print-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-remote-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-remote-3.6.1-SNAPSHOT.jar,
+  lib/cdmlib-services-3.6.1-SNAPSHOT-sources.jar,
+  lib/cdmlib-services-3.6.1-SNAPSHOT.jar,
   lib/poi-3.10-FINAL.jar,
   lib/poi-ooxml-3.10-FINAL.jar,
   lib/xmlbeans-2.3.0.jar,

diff --combined eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
index 854759021135d5a6652f588293e363a84552cd91,bcd8ff062f8d8d9861f1404cfdbe1f160bead4b7..14bdc8315c9b1d84a042e31a2e268a2c45a740c9
--- 1/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
--- 2/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.editor/META-INF/MANIFEST.MF
@@@ -2,7 -2,7 +2,7 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: Editor Bundle
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.editor;singleton:=true
- Bundle-Version: 3.5.2.qualifier
+ Bundle-Version: 3.6.1.qualifier
  Bundle-Activator: eu.etaxonomy.taxeditor.editor.internal.TaxeditorEditorPlugin
  Bundle-Vendor: %Bundle-Vendor.0
  Bundle-Localization: OSGI-INF/l10n/plugin
@@@ -25,7 -25,7 +25,7 @@@ Require-Bundle: org.eclipse.ui
   org.eclipse.zest.core,
   org.eclipse.zest.layouts,
   eu.etaxonomy.taxeditor.cdmlib,
-  org.eclipse.ui.ide;bundle-version="3.7.0"
+  org.eclipse.ui.ide
  Bundle-RequiredExecutionEnvironment: JavaSE-1.6
  Bundle-ActivationPolicy: lazy
  Import-Package: org.eclipse.core.databinding.beans,
@@@ -177,11 -177,4 +177,11 @@@ Bundle-ClassPath: .
   jdimodel.jar,
   pdebuild.jar,
   compatibility.jar,
 - junit.jar
 + junit.jar,
 + lib/biojava3-alignment-3.0.7.jar,
 + lib/biojava3-core-3.0.7.jar,
 + lib/core-1.8.5.jar,
 + lib/sequencing-1.8.5.jar,
 + lib/bioinfweb.commons/,
 + lib/LibrAlign/,
 + lib/commons-lang3-3.1.jar

diff --combined eu.etaxonomy.taxeditor.editor/plugin.xml
index 9c171a2137d2e1a25755a48885d8bf1b87fc6a66,d06b782aa811d6b29e2875ed6f37b4a6d63f1d12..ed687ff8531d18b08f56b8ad3e58cc0ccf77fd65
--- 1/eu.etaxonomy.taxeditor.editor/plugin.xml
--- 2/eu.etaxonomy.taxeditor.editor/plugin.xml
+++ b/eu.etaxonomy.taxeditor.editor/plugin.xml
@@@ -83,15 -83,8 +83,15 @@@
              id="eu.etaxonomy.taxeditor.editor.view.checklist.ChecklistEditor"
              name="%editor.name.8">
        </editor>
 +      <editor
 +            class="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"
 +            default="false"
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor"
 +            name="Alignment Editor">
 +      </editor>
     </extension>
        <extension
 +            id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
              point="org.eclipse.ui.views">
           <view
                 allowMultiple="false"
@@@ -159,15 -152,9 +159,15 @@@
                 id="eu.etaxonomy.taxeditor.editor.view.validation.problems"
                 name="%view.name.6">
           </view>
 +         <view
 +               allowMultiple="true"
 +               class="eu.etaxonomy.taxeditor.editor.molecular.PherogramViewPart"
 +               id="eu.etaxonomy.taxeditor.editor.molecular.PherogramView"
 +               name="PherogramView"
 +               restorable="true">
 +         </view>
        </extension>
 -      
 -      <!-- VALIDATION RELATED STUFF -->
 +      <!-- VALIDATION RELATED STUFF -->
        <extension point="org.eclipse.core.resources.markers" name="%extension.name.0" id="eu.etaxonomy.taxeditor.markers.validationerror">
                <super type="org.eclipse.core.resources.problemmarker"/>
                <attribute name="databaseId"/>
@@@ -239,7 -226,8 +239,7 @@@
                        name="%marker.field.7">
                </markerField>
        </extension>
 -      
 -  <extension
 +   <extension
           point="org.eclipse.ui.elementFactories">
        <factory
              class="eu.etaxonomy.taxeditor.editor.TaxonEditorInputFactory"
@@@ -337,11 -325,6 +337,11 @@@
                 </reference>
              </visibleWhen>
           </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +               label="Alignment Editor"
 +               style="push">
 +         </command>
        </menuContribution>
        <menuContribution
              locationURI="menu:org.eclipse.ui.main.menu.navigate">
@@@ -669,12 -652,12 +669,12 @@@
              <visibleWhen
                    checkEnabled="true">
                 <and>
 -                  <with
 -                        variable="selection">
 -                     <count
 -                           value="+">
 -                     </count>
 -                  </with>
 +               <with
 +                     variable="selection">
 +                  <count
 +                        value="+">
 +                  </count>
 +               </with>
                    <reference
                          definitionId="isIndividualsAssociation">
                    </reference>
@@@ -712,7 -695,7 +712,7 @@@
                 name="eu.etaxonomy.taxeditor.taxonDescriptionEditor.separator.afterNew"
                 visible="true">
           </separator>
 -                  <command
 +         <command
                 commandId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
                 label="%command.label.30"
                 style="push">
@@@ -748,28 -731,6 +748,28 @@@
                 label="%command.label.54"
                 style="push">
           </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.editSequence"
 +               label="Edit Sequence"
 +               style="push">
 +            <visibleWhen
 +                  checkEnabled="true">
 +               <reference
 +                     definitionId="isSequence">
 +               </reference>
 +            </visibleWhen>
 +         </command>
 +         <command
 +               commandId="eu.etaxonomy.taxeditor.editor.showPherogram"
 +               label="Show Pherogram"
 +               style="push">
 +            <visibleWhen
 +                  checkEnabled="true">
 +               <reference
 +                     definitionId="isSingleRead">
 +               </reference>
 +            </visibleWhen>
 +         </command>
           <dynamic
                 class="eu.etaxonomy.taxeditor.editor.view.derivate.contextMenu.DerivateViewContextMenu"
                 id="eu.etaxonomy.taxeditor.editor.view.derivate.DerivateContextMenu">
@@@ -982,67 -943,11 +982,67 @@@
                 style="push">
              <visibleWhen>
                 <reference
-                      definitionId="isGroup">
+                      definitionId="isGroupEditor">
                 </reference>
              </visibleWhen>
           </command>
        </menuContribution>
 +      <menuContribution
 +            allPopups="false"
 +            locationURI="menu:org.eclipse.ui.main.menu">
 +         <menu
 +               label="Alignment Editor">
 +            <command
 +                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
 +                  label="Load Pherogram"
 +                  style="push">
 +            </command>
 +            <visibleWhen
 +                  checkEnabled="true">
 +               <with
 +                     variable="activePartId">
 +                  <equals
 +                        value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                  </equals>
 +               </with>
 +            </visibleWhen>
 +         </menu>
 +      </menuContribution>
 +      <menuContribution
 +            locationURI="toolbar:org.eclipse.ui.main.toolbar?after=eu.etaxonomy.taxeditor.navigation.search.toolbar">
 +         <toolbar
 +               id="eu.etaxonomy.taxeditor.editor.alignmentToolbar">
 +            <command
 +                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite"
 +                  label="Toggle insert/overwrite"
 +                  style="push">
 +               <visibleWhen
 +                     checkEnabled="true">
 +                  <with
 +                        variable="activePartId">
 +                     <equals
 +                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                     </equals>
 +                  </with>
 +               </visibleWhen>
 +            </command>
 +            <command
 +                  commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion"
 +                  icon="icons/pherogram-insert-left-16x16.png"
 +                  style="push">
 +               <visibleWhen
 +                     checkEnabled="true">
 +                  <with
 +                        variable="activePartId">
 +                     <equals
 +                           value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +                     </equals>
 +                  </with>
 +               </visibleWhen>
 +            </command>
 +         </toolbar>
 +      </menuContribution>
 +      
        <menuContribution
              allPopups="false"
              locationURI="toolbar:eu.etaxonomy.taxeditor.editor.view.descriptive">
@@@ -1145,8 -1050,8 +1145,8 @@@
                        value="eu.etaxonomy.taxeditor.editor.view.uses">
                                </equals>
                  </or>
 -               </with>
 -         </activeWhen>
 +             </with>
 +          </activeWhen>
        </handler>
        <handler
              class="eu.etaxonomy.taxeditor.editor.key.polytomous.handler.DeleteNodeHandler"
@@@ -1176,18 -1081,6 +1176,18 @@@
              class="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
              commandId="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler">
        </handler>
 +      <handler
 +            class="eu.etaxonomy.taxeditor.editor.handler.LoadPherogramHandler"
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram">
 +         <activeWhen>
 +            <with
 +                  variable="activePartId">
 +               <equals
 +                     value="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor">
 +               </equals>
 +            </with>
 +         </activeWhen>
 +      </handler>
        <handler
              class="eu.etaxonomy.taxeditor.editor.view.derivate.handler.DeleteDerivateHandler"
              commandId="eu.etaxonomy.taxeditor.editor.view.derivate.command.delete">
@@@ -1216,14 -1109,6 +1216,14 @@@
              class="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.ToggleShowOnlyIndividualAssociationsHandler"
              commandId="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations">
        </handler>
 +      <handler
 +            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleInsertOverwriteHandler"
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite">
 +      </handler>
 +      <handler
 +            class="eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleLeftRightInsertionHandler"
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion">
 +      </handler>
     </extension>
     <extension
           name="%extension.name"
@@@ -1291,7 -1176,7 +1291,7 @@@
              id="eu.etaxonomy.taxeditor.editor.name.swapSynonymAndAccepted"
              name="%command.name.6">
        </command>
 -      <command
 +       <command
              categoryId="eu.etaxonomy.taxeditor.editor.taxon.name.command.category"
              defaultHandler="eu.etaxonomy.taxeditor.editor.name.handler.MoveSynonymToAnotherAcceptedTaxonHandler"
              id="eu.etaxonomy.taxeditor.editor.name.moveSynonymToAnotherAcceptedTaxon"
@@@ -1343,8 -1228,8 +1343,8 @@@
              id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.adddescription"
              name="%command.name.11">
        </command>
 -       <command
 -             categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
 +      <command
 +            categoryId="eu.etaxonomy.taxeditor.editor.view.descriptive.command.category"
               defaultHandler="eu.etaxonomy.taxeditor.editor.view.descriptive.handler.DeleteHandler"
               id="eu.etaxonomy.taxeditor.editor.view.descriptive.command.delete"
               name="%command.name.48">
@@@ -1517,34 -1402,17 +1517,34 @@@
               defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistEditorHandler"
               id="eu.etaxonomy.taxeditor.editor.handler.OpenChecklistViewHandler"
               name="%command.name.38">
 -       </command>
 +      </command>
        <command
              categoryId="eu.etaxonomy.taxeditor.editor.new.category"
              defaultHandler="eu.etaxonomy.taxeditor.view.datasource.handler.CreateDataSourceHandler"
              id="eu.etaxonomy.taxeditor.editor.command.new.datasource"
              name="%command.name.39">
        </command>
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditorHandler"
 +            id="eu.etaxonomy.taxeditor.editor.handler.OpenAlignmentEditor"
 +            name="Open Alignment Editor">
 +      </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
 +            name="Load Pherogram">
 +      </command>
        <command
              id="eu.etaxonomy.taxeditor.editor.handler.showOnlyIndividualAssociations"
              name="%command.name.41">
        </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleInsertOverwrite"
 +            name="Toggle insert/overwrite">
 +      </command>
 +      <command
 +            id="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.toggleLeftRightInsertion"
 +            name="Toggle left/right insertion in base call sequence">
 +      </command>
        <command
              defaultHandler="eu.etaxonomy.taxeditor.editor.handler.OpenTaxonEditorHandler"
              id="eu.etaxonomy.taxeditor.editor.openTaxonEditor"
@@@ -1583,16 -1451,7 +1583,16 @@@
              id="eu.etaxonomy.taxeditor.description.commands.moveDescriptionElements"
              name="%command.name.12">
        </command>
 -        
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.EditSequenceHandler"
 +            id="eu.etaxonomy.taxeditor.editor.editSequence"
 +            name="Edit Sequence">
 +      </command>
 +      <command
 +            defaultHandler="eu.etaxonomy.taxeditor.editor.handler.ShowPherogramHandler"
 +            id="eu.etaxonomy.taxeditor.editor.showPherogram"
 +            name="Show Pherogram">
 +      </command>
     </extension>
     <extension
           point="org.eclipse.core.expressions.definitions">
@@@ -1741,11 -1600,11 +1741,11 @@@
           </with>
        </definition>
        <definition
-             id="isGroup">
+             id="isGroupEditor">
           <with
                 variable="activeEditor">
              <test
-                   property="taxeditor-bulkeditor.propertyTester.isGroup">
+                   property="taxeditor-bulkeditor.propertyTester.isGroupEditor">
              </test>
           </with>
        </definition>
@@@ -1758,24 -1617,6 +1758,24 @@@
              </test>
           </with>
        </definition>
 +      <definition
 +            id="isSequence">
 +         <with
 +               variable="selection">
 +            <test
 +                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSequence">
 +            </test>
 +         </with>
 +      </definition>
 +      <definition
 +            id="isSingleRead">
 +         <with
 +               variable="selection">
 +            <test
 +                  property="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester.isSingleRead">
 +            </test>
 +         </with>
 +      </definition>
     </extension>
     <extension
           point="org.eclipse.core.expressions.propertyTesters">
@@@ -1797,16 -1638,9 +1797,16 @@@
              class="eu.etaxonomy.taxeditor.bulkeditor.command.BulkEditorPropertyTester"
              id="taxeditor-bulkeditor.PropertyTester"
              namespace="taxeditor-bulkeditor.propertyTester"
-             properties="isGroup"
+             properties="isGroupEditor"
              type="eu.etaxonomy.taxeditor.bulkeditor.BulkEditor">
        </propertyTester>
 +      <propertyTester
 +            class="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
 +            id="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
 +            namespace="eu.etaxonomy.taxeditor.editor.handler.SpecimenPropertyTester"
 +            properties="isSequence,isSingleRead"
 +            type="org.eclipse.jface.viewers.IStructuredSelection">
 +      </propertyTester>
     </extension>
     <extension
           point="org.eclipse.ui.bindings">   
@@@ -1815,11 -1649,6 +1815,11 @@@
              id="eu.etaxonomy.taxeditor.bindings.scheme.default"
              name="%scheme.name">
        </scheme>
 +      <key
 +            commandId="eu.etaxonomy.taxeditor.editor.molecular.AlignmentEditor.loadPherogram"
 +            schemeId="eu.etaxonomy.taxeditor.bindings.scheme.default"
 +            sequence="M1+O">
 +      </key>
     </extension>
      <extension
           point="org.eclipse.ui.importWizards">

diff --combined eu.etaxonomy.taxeditor.test/META-INF/MANIFEST.MF
index d52b5b19652facf363dc8d581834fb310a3ac39e,dd55c822551cf19c70da92cb4b1f3e0c86ff48c9..4d33cf2f602b5d8a87980dbe33796788f829cb37
--- 1/eu.etaxonomy.taxeditor.test/META-INF/MANIFEST.MF
--- 2/eu.etaxonomy.taxeditor.test/META-INF/MANIFEST.MF
+++ b/eu.etaxonomy.taxeditor.test/META-INF/MANIFEST.MF
@@@ -2,24 -2,23 +2,24 @@@ Manifest-Version: 1.
  Bundle-ManifestVersion: 2
  Bundle-Name: eu.etaxonomy.taxeditor.test
  Bundle-SymbolicName: eu.etaxonomy.taxeditor.test;singleton:=true
- Bundle-Version: 3.4.0.qualifier
+ Bundle-Version: 3.6.1.qualifier
  Bundle-ActivationPolicy: lazy
  Bundle-Vendor: EDIT
  Bundle-RequiredExecutionEnvironment: JavaSE-1.6
  Require-Bundle: org.apache.log4j,
-  org.eclipse.ui;bundle-version="3.6.2",
-  org.eclipse.core.runtime;bundle-version="3.6.0",
+  org.eclipse.ui,
+  org.eclipse.core.runtime,
 - org.eclipse.swtbot.eclipse.core,
 + org.eclipse.swtbot.eclipse.core;bundle-version="2.0.5",
   org.eclipse.swtbot.eclipse.finder,
   org.eclipse.swtbot.junit4_x,
   org.eclipse.ui.ide,
-  org.junit4,
-  eu.etaxonomy.taxeditor.application;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.bulkeditor;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.cdmlib;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.editor;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.help;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.navigation;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.printpublisher;bundle-version="3.0.6",
-  eu.etaxonomy.taxeditor.store;bundle-version="3.0.6"
+  eu.etaxonomy.taxeditor.application,
+  eu.etaxonomy.taxeditor.bulkeditor,
+  eu.etaxonomy.taxeditor.cdmlib,
+  eu.etaxonomy.taxeditor.editor,
+  eu.etaxonomy.taxeditor.help,
+  eu.etaxonomy.taxeditor.navigation,
+  eu.etaxonomy.taxeditor.printpublisher,
+  eu.etaxonomy.taxeditor.store
  Eclipse-RegisterBuddy: org.apache.log4j
++Import-Package: org.junit.runner