diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 42b874b46cc..cf744de21bc 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -271,6 +271,10 @@
     <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/>
     <!-- Excel datatypes -->
     <datatype extension="xlsx" type="galaxy.datatypes.binary:Xlsx" display_in_upload="true" />
+    <!-- MSA Datatypes -->
+    <datatype extension="hmm2" type="galaxy.datatypes.msa:Hmmer2" display_in_upload="true" />
+    <datatype extension="hmm3" type="galaxy.datatypes.msa:Hmmer3" display_in_upload="true" />
+    <datatype extension="stockholm" type="galaxy.datatypes.msa:Stockholm_1_0" display_in_upload="True" />
   </registration>
   <sniffers>
     <!--
@@ -316,6 +320,9 @@
     <sniffer type="galaxy.datatypes.text:Ipynb"/>
     <sniffer type="galaxy.datatypes.text:Json"/>
     <sniffer type="galaxy.datatypes.sequence:RNADotPlotMatrix"/>
+    <sniffer type="galaxy.datatypes.msa:Hmmer2" />
+    <sniffer type="galaxy.datatypes.msa:Hmmer3" />
+    <sniffer type="galaxy.datatypes.msa:Stockholm_1_0" />
     <sniffer type="galaxy.datatypes.images:Jpg"/>
     <sniffer type="galaxy.datatypes.images:Png"/>
     <sniffer type="galaxy.datatypes.images:Tiff"/>
diff --git a/lib/galaxy/datatypes/msa.py b/lib/galaxy/datatypes/msa.py
new file mode 100644
index 00000000000..011de5a720f
--- /dev/null
+++ b/lib/galaxy/datatypes/msa.py
@@ -0,0 +1,168 @@
+from galaxy.datatypes.data import Text
+from galaxy.datatypes.binary import Binary
+from galaxy.datatypes.data import get_file_peek
+from galaxy.datatypes.data import nice_size
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.util import generic_util
+import os
+
+
+import logging
+log = logging.getLogger(__name__)
+
+
+class Hmmer( Text ):
+    file_ext = "hmm"
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            dataset.blurb = "HMMER Database"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disc'
+
+    def display_peek(self, dataset):
+        try:
+            return dataset.peek
+        except:
+            return "HMMER database (%s)" % ( nice_size( dataset.get_size() ) )
+
+
+class Hmmer2( Hmmer ):
+
+    def sniff(self, filename):
+        """HMMER2 files start with HMMER2.0
+        """
+        with open(filename, 'r') as handle:
+            return handle.read(8) == 'HMMER2.0'
+        return False
+
+
+class Hmmer3( Hmmer ):
+
+    def sniff(self, filename):
+        """HMMER3 files start with HMMER3/f
+        """
+        with open(filename, 'r') as handle:
+            return handle.read(8) == 'HMMER3/f'
+        return False
+
+
+class HmmerPress( Binary ):
+    """Class for hmmpress database files."""
+    file_ext = 'hmmpress'
+    allow_datatype_change = False
+    composite_type = 'basic'
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        """Set the peek and blurb text."""
+        if not dataset.dataset.purged:
+            dataset.peek = "HMMER Binary database"
+            dataset.blurb = "HMMER Binary database"
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def display_peek( self, dataset ):
+        """Create HTML content, used for displaying peek."""
+        try:
+            return dataset.peek
+        except:
+            return "HMMER3 database (multiple files)"
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+        # Binary model
+        self.add_composite_file('model.hmm.h3m', is_binary=True)
+        # SSI index for binary model
+        self.add_composite_file('model.hmm.h3i', is_binary=True)
+        # Profiles (MSV part)
+        self.add_composite_file('model.hmm.h3f', is_binary=True)
+        # Profiles (remained)
+        self.add_composite_file('model.hmm.h3p', is_binary=True)
+
+Binary.register_unsniffable_binary_ext("hmmpress")
+
+
+class Stockholm_1_0( Text ):
+    file_ext = "stockholm"
+
+    MetadataElement( name="number_of_alignments", default=0, desc="Number of multiple alignments", readonly=True, visible=True, optional=True, no_value=0 )
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            if (dataset.metadata.number_of_models == 1):
+                dataset.blurb = "1 alignment"
+            else:
+                dataset.blurb = "%s alignments" % dataset.metadata.number_of_models
+            dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disc'
+
+    def sniff( self, filename ):
+        if generic_util.count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', filename) > 0:
+            return True
+        else:
+            return False
+
+    def set_meta( self, dataset, **kwd ):
+        """
+
+        Set the number of models in dataset.
+        """
+        dataset.metadata.number_of_models = generic_util.count_special_lines('^#[[:space:]+]STOCKHOLM[[:space:]+]1.0', dataset.file_name)
+
+    def split( cls, input_datasets, subdir_generator_function, split_params):
+        """
+
+        Split the input files by model records.
+        """
+        if split_params is None:
+            return None
+
+        if len(input_datasets) > 1:
+            raise Exception("STOCKHOLM-file splitting does not support multiple files")
+        input_files = [ds.file_name for ds in input_datasets]
+
+        chunk_size = None
+        if split_params['split_mode'] == 'number_of_parts':
+            raise Exception('Split mode "%s" is currently not implemented for STOCKHOLM-files.' % split_params['split_mode'])
+        elif split_params['split_mode'] == 'to_size':
+            chunk_size = int(split_params['split_size'])
+        else:
+            raise Exception('Unsupported split mode %s' % split_params['split_mode'])
+
+        def _read_stockholm_records( filename ):
+            lines = []
+            with open(filename) as handle:
+                for line in handle:
+                    lines.append( line )
+                    if line.strip() == '//':
+                        yield lines
+                        lines = []
+
+        def _write_part_stockholm_file( accumulated_lines ):
+            part_dir = subdir_generator_function()
+            part_path = os.path.join( part_dir, os.path.basename( input_files[0] ) )
+            part_file = open( part_path, 'w' )
+            part_file.writelines( accumulated_lines )
+            part_file.close()
+
+        try:
+
+            stockholm_records = _read_stockholm_records( input_files[0] )
+            stockholm_lines_accumulated = []
+            for counter, stockholm_record in enumerate( stockholm_records, start=1):
+                stockholm_lines_accumulated.extend( stockholm_record )
+                if counter % chunk_size == 0:
+                    _write_part_stockholm_file( stockholm_lines_accumulated )
+                    stockholm_lines_accumulated = []
+            if stockholm_lines_accumulated:
+                _write_part_stockholm_file( stockholm_lines_accumulated )
+        except Exception, e:
+            log.error('Unable to split files: %s' % str(e))
+            raise
+    split = classmethod(split)
diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py
index 856096292c4..d6211c89021 100644
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -23,6 +23,7 @@ import assembly
 import ngsindex
 import graph
 import text
+import msa
 import galaxy.util
 from galaxy.util.odict import odict
 from display_applications.application import DisplayApplication
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
index 7309e84afd0..a3e3efd1828 100644
--- a/lib/galaxy/datatypes/text.py
+++ b/lib/galaxy/datatypes/text.py
@@ -139,7 +139,7 @@ class Obo( Text ):
 
     def sniff( self, filename ):
         """
-            Try to guess the Obo filetype. 
+            Try to guess the Obo filetype.
             It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
         """
         stanza = re.compile(r'^\[.*\]$')
@@ -158,7 +158,7 @@ class Obo( Text ):
 
 class Arff( Text ):
     """
-        An ARFF (Attribute-Relation File Format) file is an ASCII text file that describes a list of instances sharing a set of attributes. 
+        An ARFF (Attribute-Relation File Format) file is an ASCII text file that describes a list of instances sharing a set of attributes.
         http://weka.wikispaces.com/ARFF
     """
     file_ext = "arff"
@@ -179,7 +179,7 @@ class Arff( Text ):
 
     def sniff( self, filename ):
         """
-            Try to guess the Arff filetype. 
+            Try to guess the Arff filetype.
             It usually starts with a "format-version:" string and has several stanzas which starts with "id:".
         """
         with open( filename ) as handle:
@@ -318,7 +318,7 @@ class SnpSiftDbNSFP( Text ):
     composite_type = 'auto_primary_file'
     allow_datatype_change = False
     """
-    ## The dbNSFP file is a tabular file with 1 header line 
+    ## The dbNSFP file is a tabular file with 1 header line
     ## The first 4 columns are required to be: chrom	pos	ref	alt
     ## These match columns 1,2,4,5 of the VCF file
     ## SnpSift requires the file to be block-gzipped and the indexed with samtools tabix
@@ -335,14 +335,14 @@ class SnpSiftDbNSFP( Text ):
     def init_meta( self, dataset, copy_from=None ):
         Text.init_meta( self, dataset, copy_from=copy_from )
     def generate_primary_file( self, dataset = None ):
-        """ 
+        """
         This is called only at upload to write the html file
         cannot rename the datasets here - they come with the default unfortunately
         """
         self.regenerate_primary_file( dataset )
     def regenerate_primary_file(self,dataset):
         """
-        cannot do this until we are setting metadata 
+        cannot do this until we are setting metadata
         """
         annotations = "dbNSFP Annotations: %s\n" % ','.join(dataset.metadata.annotation)
         f = open(dataset.file_name,'a')
@@ -366,7 +366,7 @@ class SnpSiftDbNSFP( Text ):
                             lines = buf.splitlines()
                             headers = lines[0].split('\t')
                             dataset.metadata.annotation = headers[4:]
-                        except Exception,e:        
+                        except Exception,e:
                             log.warn("set_meta fname: %s  %s" % (fname,str(e)))
                         finally:
                             fh.close()
@@ -375,4 +375,3 @@ class SnpSiftDbNSFP( Text ):
             self.regenerate_primary_file(dataset)
         except Exception,e:
             log.warn("set_meta fname: %s  %s" % (dataset.file_name if dataset and dataset.file_name else 'Unkwown',str(e)))
-
diff --git a/lib/galaxy/datatypes/util/generic_util.py b/lib/galaxy/datatypes/util/generic_util.py
new file mode 100644
index 00000000000..49bfd007a89
--- /dev/null
+++ b/lib/galaxy/datatypes/util/generic_util.py
@@ -0,0 +1,19 @@
+import subprocess
+
+
+def count_special_lines( word, filename, invert=False ):
+    """
+        searching for special 'words' using the grep tool
+        grep is used to speed up the searching and counting
+        The number of hits is returned.
+    """
+    try:
+        cmd = ["grep", "-c"]
+        if invert:
+            cmd.append('-v')
+        cmd.extend([word, filename])
+        out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
+        return int(out.communicate()[0].split()[0])
+    except:
+        pass
+    return 0