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.  In Dfam 3.8 this format became taxonomically partitioned
     to make it possible to download only portions of the database at a time.
     Please see the FamDB/README for more information on how to use this
     format.

  o HMM Files for use with nhmmer:
      - Dfam.hmm.gz : 

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

       !!!! This is a 92GB file compressed and should only be downloaded if    !!!!
       !!!! the entire Dfam database (curated + uncurated ) families           !!!!
       !!!! are needed.  Uncompressed, 818GB will be needed to store the file. !!!!

      - Dfam_curatedonly.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_curatedonly.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/Dfam_3.7/userman.txt


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

RepeatMasker (4.1.6) ships with a copy of Dfam (root partition only) in FamDB format. This 
can be replaced with a newer version of Dfam, or additional taxanomic paritions may be 
added at a later time.