SSU-ALIGN - structural alignment of SSU rRNA sequences
Copyright (C) 2016 HHMI Janelia Farm Research Campus
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SSU-ALIGN is a software package for creating, masking and visualizing
small subunit ribosomal RNA (SSU rRNA) multiple sequence
alignments. It uses profile probabilistic models called "profile
hidden Markov models" (profile HMMs) and "covariance models" (CMs)
that represent archaeal 16S SSU rRNA, bacterial 16S SSU rRNA and
eukaryotic 18S SSU rRNA. Each of these profile models was built from a
reference alignment derived from Robin Gutell's Comparative RNA
Website database (CRW) (Cannone et al., BMC Bionformatics. 2002; 3:2.)
as described in the user's guide. The alignments created by SSU-ALIGN
explicitly take into account the conserved secondary structure of SSU
as annotated by CRW.

Other files to read in the top-level source directory:

    INSTALL          Brief installation instructions.
    Userguide.pdf    The SSU-ALIGN User's Guide.
    COPYRIGHT        Copyright and license information.
    LICENSE          The GNU General Public License (GPLv3).

To get started after installation, see the Tutorial section in the
SSU-ALIGN User's Guide (Userguide.pdf).

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Eric Nawrocki
nawrocke@ncbi.nlm.nih.gov