diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 6782d490ae0..64bb6dd7c20 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -631,18 +631,27 @@
     <datatype extension="maskinfo-asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" subclass="true" display_in_upload="true" />
     <datatype extension="pssm-asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" subclass="true" display_in_upload="true" />
     <!-- PlantTribes datatypes -->
+    <!--
+    The commented entries in this section are required by versions 1.0.0, 1.0.1 and 1.0.2 of the
+    PlantTribes tools in the MTS Phylogenetics category, and are not required by version 1.0.3 of
+    later.  These datatypes will be removed in a future Galaxy release.  
+    -->
+    <!--
     <datatype extension="ptalign" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignment" />
     <datatype extension="ptalignca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentCodonAlignment" />
     <datatype extension="ptaligntrimmed" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmed" />
     <datatype extension="ptaligntrimmedca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment" />
     <datatype extension="ptalignfiltered" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFiltered" />
     <datatype extension="ptalignfilteredca" type="galaxy.datatypes.plant_tribes:PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment" />
+    -->
     <datatype extension="ptkscmp" type="galaxy.datatypes.plant_tribes:PlantTribesKsComponents" display_in_upload="true"/>
+    <!--
     <datatype extension="ptortho" type="galaxy.datatypes.plant_tribes:PlantTribesOrtho" />
     <datatype extension="ptorthocs" type="galaxy.datatypes.plant_tribes:PlantTribesOrthoCodingSequence" />
     <datatype extension="ptphylip" type="galaxy.datatypes.plant_tribes:PlantTribesPhylip" />
     <datatype extension="pttgf" type="galaxy.datatypes.plant_tribes:PlantTribesTargetedGeneFamilies" />
     <datatype extension="pttree" type="galaxy.datatypes.plant_tribes:PlantTribesPhylogeneticTree" />
+    -->
     <datatype extension="smat" type="galaxy.datatypes.plant_tribes:Smat" display_in_upload="true" />
     <!-- Start Haplotype / LOD Datatypes -->
     <datatype extension="alohomora_gts" type="galaxy.datatypes.genetics:GenotypeMatrix" />
diff --git a/lib/galaxy/datatypes/plant_tribes.py b/lib/galaxy/datatypes/plant_tribes.py
index 983600a86b9..1b804160970 100644
--- a/lib/galaxy/datatypes/plant_tribes.py
+++ b/lib/galaxy/datatypes/plant_tribes.py
@@ -1,12 +1,10 @@
 import logging
-import os
 import re
 
 from galaxy.datatypes.data import get_file_peek, Text
-from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
+from galaxy.datatypes.metadata import MetadataElement
 from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.tabular import Tabular
-from galaxy.datatypes.text import Html
 from galaxy.util import nice_size
 
 log = logging.getLogger(__name__)
@@ -75,20 +73,24 @@ class Smat(Text):
         return True
 
 
-class PlantTribes(Html):
-    """
-    PlantTribes abstract class.
-    """
-    composite_type = 'basic'
-    MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
-
-    def set_meta(self, dataset, overwrite=True, **kwd):
-        try:
-            efp = dataset.extra_files_path
-            if os.path.exists(efp):
-                dataset.metadata.num_files = len(os.listdir(efp))
-        except Exception as e:
-            log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
+# These commented classes are required by versions 1.0.0, 1.0.1 and 1.0.2 of the
+# PlantTribes tools in the MTS Phylogenetics category, and are not required by
+# version 1.0.3 or later.  These datatypes will be removed in a future Galaxy release.
+#
+# class PlantTribes(Html):
+#    """
+#    PlantTribes abstract class.
+#    """
+#    composite_type = 'basic'
+#    MetadataElement(name="num_files", default=0, desc="Number of files in files_path directory", param=MetadataParameter, readonly=True, visible=False, no_value=0)
+#
+#    def set_meta(self, dataset, overwrite=True, **kwd):
+#        try:
+#            efp = dataset.extra_files_path
+#            if os.path.exists(efp):
+#                dataset.metadata.num_files = len(os.listdir(efp))
+#        except Exception as e:
+#            log.warning("set_meta fname: %s %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown', str(e)))
 
 
 class PlantTribesKsComponents(Tabular):
@@ -150,126 +152,125 @@ class PlantTribesKsComponents(Tabular):
         except Exception:
             return False
 
-
-class PlantTribesOrtho(PlantTribes):
-    """
-    PlantTribes sequences classified into precomputed, orthologous gene family
-    clusters.
-    """
-    file_ext = "ptortho"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesOrtho, self).set_peek(dataset)
-        dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesOrthoCodingSequence(PlantTribes):
-    """
-    PlantTribes sequences classified into precomputed, orthologous gene family
-    clusters and corresponding coding sequences.
-    """
-    file_ext = "ptorthocs"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesOrthoCodingSequence, self).set_peek(dataset)
-        dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesTargetedGeneFamilies(PlantTribes):
-    """
-    PlantTribes targeted gene families.
-    """
-    file_ext = "pttgf"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset)
-        dataset.blurb = "Targeted gene families"
-
-
-class PlantTribesPhylogeneticTree(PlantTribes):
-    """
-    PlantTribes multiple sequence alignments and inferred maximum likelihood
-    phylogenies for orthogroups.
-    """
-    file_ext = "pttree"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesPhylogeneticTree, self).set_peek(dataset)
-        dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesPhylip(PlantTribes):
-    """
-    PlantTribes orthogroup phylip multiple sequence alignments.
-    """
-    file_ext = "ptphylip"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesPhylip, self).set_peek(dataset)
-        dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesMultipleSequenceAlignment(PlantTribes):
-    """
-    PlantTribes multiple sequence alignments.
-    """
-    file_ext = "ptalign"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset)
-        dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
-    """
-    PlantTribes multiple sequence alignments with codon alignments.
-    """
-    file_ext = "ptalignca"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset)
-        dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
-    """
-    PlantTribes trimmed multiple sequence alignments.
-    """
-    file_ext = "ptaligntrimmed"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset)
-        dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
-    """
-    PlantTribes trimmed multiple sequence alignments with codon alignments.
-    """
-    file_ext = "ptaligntrimmedca"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset)
-        dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
-    """
-    PlantTribes filtered multiple sequence alignments.
-    """
-    file_ext = "ptalignfiltered"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset)
-        dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
-
-
-class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
-    """
-    PlantTribes filtered multiple sequence alignments with codon alignments.
-    """
-    file_ext = "ptalignfilteredca"
-
-    def set_peek(self, dataset, is_multi_byte=False):
-        super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset)
-        dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+# class PlantTribesOrtho(PlantTribes):
+#    """
+#    PlantTribes sequences classified into precomputed, orthologous gene family
+#    clusters.
+#    """
+#    file_ext = "ptortho"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesOrtho, self).set_peek(dataset)
+#        dataset.blurb = "Proteins orthogroup fasta files: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesOrthoCodingSequence(PlantTribes):
+#    """
+#    PlantTribes sequences classified into precomputed, orthologous gene family
+#    clusters and corresponding coding sequences.
+#    """
+#    file_ext = "ptorthocs"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesOrthoCodingSequence, self).set_peek(dataset)
+#        dataset.blurb = "Protein and coding sequences orthogroup fasta files: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesTargetedGeneFamilies(PlantTribes):
+#    """
+#    PlantTribes targeted gene families.
+#    """
+#    file_ext = "pttgf"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesTargetedGeneFamilies, self).set_peek(dataset)
+#        dataset.blurb = "Targeted gene families"
+#
+#
+# class PlantTribesPhylogeneticTree(PlantTribes):
+#    """
+#    PlantTribes multiple sequence alignments and inferred maximum likelihood
+#    phylogenies for orthogroups.
+#    """
+#    file_ext = "pttree"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesPhylogeneticTree, self).set_peek(dataset)
+#        dataset.blurb = "Phylogenetic trees: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesPhylip(PlantTribes):
+#    """
+#    PlantTribes orthogroup phylip multiple sequence alignments.
+#    """
+#    file_ext = "ptphylip"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesPhylip, self).set_peek(dataset)
+#        dataset.blurb = "Orthogroup phylip multiple sequence alignments: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesMultipleSequenceAlignment(PlantTribes):
+#    """
+#    PlantTribes multiple sequence alignments.
+#    """
+#    file_ext = "ptalign"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesMultipleSequenceAlignment, self).set_peek(dataset)
+#        dataset.blurb = "Proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesMultipleSequenceAlignmentCodonAlignment(PlantTribes):
+#    """
+#    PlantTribes multiple sequence alignments with codon alignments.
+#    """
+#    file_ext = "ptalignca"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesMultipleSequenceAlignmentCodonAlignment, self).set_peek(dataset)
+#        dataset.blurb = "Protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesMultipleSequenceAlignmentTrimmed(PlantTribes):
+#    """
+#    PlantTribes trimmed multiple sequence alignments.
+#    """
+#    file_ext = "ptaligntrimmed"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesMultipleSequenceAlignmentTrimmed, self).set_peek(dataset)
+#        dataset.blurb = "Trimmed proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment(PlantTribes):
+#    """
+#    PlantTribes trimmed multiple sequence alignments with codon alignments.
+#    """
+#    file_ext = "ptaligntrimmedca"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesMultipleSequenceAlignmentTrimmedCodonAlignment, self).set_peek(dataset)
+#        dataset.blurb = "Trimmed protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesMultipleSequenceAlignmentFiltered(PlantTribes):
+#    """
+#    PlantTribes filtered multiple sequence alignments.
+#    """
+#    file_ext = "ptalignfiltered"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesMultipleSequenceAlignmentFiltered, self).set_peek(dataset)
+#        dataset.blurb = "Filtered proteins orthogroup alignments: %d items" % dataset.metadata.num_files
+#
+#
+# class PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment(PlantTribes):
+#    """
+#    PlantTribes filtered multiple sequence alignments with codon alignments.
+#    """
+#    file_ext = "ptalignfilteredca"
+#
+#    def set_peek(self, dataset, is_multi_byte=False):
+#        super(PlantTribesMultipleSequenceAlignmentFilteredCodonAlignment, self).set_peek(dataset)
+#        dataset.blurb = "Filtered protein and coding sequences orthogroup alignments: %d items" % dataset.metadata.num_files