Dfam Family Files
=================

There are several ways to access Dfam families.  We provide a website
for detailed exploration at http://dfam.org, we offer an API for programmatic
access to the database at http://dfam.org/api ( docs: http://dfam.org/help/api ),
and we offer several options for offline access:

  o FamDB 
    
     FamDB is a HDF5 based export format designed for efficient storage and
     retrieval of Dfam data for offline use.  The V3 format provides
     the full Dfam export in components and partitions. Components are
     are divided into model-type and curation status:

         - Curated-consensus (CC): The consensus sequences (and metadata) for
           the curated [DF families] in Dfam.
         - Uncurated-consensus (UC): The consensus sequences (and metadata) 
           for the uncurated [DR families] in Dfam.
         - Curated-HMM (CH): The profile HMMs (and metadata) for the curated
           formed [DF families] in Dfam.
         - Uncurated-HMM (UH): The profile HMMs (and metadata) for the uncurated
           formed [DR families] in Dfam.

     Each component further divided by taxonomic partitions to further reduce
     the size of downloads. This two-tier segmentation allows for smaller 
     downloads for the most common use-cases. For example, if you are only 
     interested in the curated consensus sequences you can download only the
     CC component which currently conveniently fits in a single partition file. 

     All components and parititions are optional and may be loaded in any 
     combination.  The only file required to use FamDB is the root partition
     which contains the component and partition metadata for a given release.
     Please see the FamDB/README.txt for more information on how to use this 
     format.


  o HMM Files for use with nhmmer:

      - Dfam-#.hmm.gz : 

        Files containing profile HMMs for *all* Dfam families (DF [curated], and 
        DR [uncurated ).  See the userman.txt file for details on the HMM format.

      - Dfam-curated_only-#.hmm.gz :

        A file containing profile HMMs for curated Dfam families (DF records only).


  o EMBL files for use with consensus-based tools:

      - Dfam-#.embl.gz

        A file containing EMBL records for *all* Dfam families (DF [curated], and 
        DR [uncurated ).

      - Dfam-curated_only-#.embl.gz

        A file containing EMBL records for curated Dfam families (DF records only).


A md5sum file ( `*.md5sum` ) is provided for each product for download validation.

For more information on the metadata in the EMBL and HMM files, see Dfam's userman.txt [3].

[1]: http://hmmer.org/
[2]: https://github.com/Dfam-consortium/FamDB/
[3]: https://www.dfam.org/releases/current/userman.txt


Using Dfam with RepeatMasker
============================

RepeatMasker (4.2.4) and future versions will no longer be packaged together with the FamDB
tool/data. This will allow users to download FamDB separately and update one or the other as
needed.  RepeatMasker will still work without FamDB provided users have custom library files
to search with.


Deprecated Support Files
========================

Previous releases of RepeatModeler uses these reference files for classification.  Newer 
versions obtain this data from FamdDB directly.  These are Dfam 3.9 versions here to 
avoid breaking older versions of Repeatmodeler.

  WARNING: Dfam 3.9 versions
  --------------------------
  Dfam-RepeatMasker.lib.gz
  RepeatPeps.lib.gz