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 partitions:
    
     The FamDB directory contains the full export of Dfam in the FamDB HDF5 
     file format. This format is taxonomically partitioned to make it
     possible to download only relevant portions of the database at a time.
     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 ).

            Dfam-1.hmm.gz,  Uncompressed Size: 99999907357
            Dfam-2.hmm.gz,  Uncompressed Size: 99999586616
            Dfam-3.hmm.gz,  Uncompressed Size: 99999987029
            Dfam-4.hmm.gz,  Uncompressed Size: 99999862893
            Dfam-5.hmm.gz,  Uncompressed Size: 99997393018
            Dfam-6.hmm.gz,  Uncompressed Size: 99999997225
            Dfam-7.hmm.gz,  Uncompressed Size: 99999731509
            Dfam-8.hmm.gz,  Uncompressed Size: 99999773942
            Dfam-9.hmm.gz,  Uncompressed Size: 99998385290
            Dfam-10.hmm.gz, Uncompressed Size: 70244800639

      - Dfam-curated_only-1.hmm.gz, Uncompressed Size: 9112881702

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

  o EMBL files for use with consensus-based tools:
      - Dfam-1.embl.gz, Uncompressed Size: 12201528386

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

      - Dfam-curated_only-1.embl.gz, Uncompressed Size: 104139495

        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 (4.1.8) ships with a copy of Dfam (root partition only) in FamDB format. This 
can be replaced with a newer version of Dfam, or additional taxonomic paritions may be 
added at a later time.