SSU-ALIGN: structural alignment of SSU rRNA sequences


SSU-ALIGN is a software package for identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S small subunit ribosomal RNA (SSU rRNA) sequences. It includes and uses the Infernal software package for generating alignments based on the conserved secondary structure and sequence of SSU rRNA. SSU-ALIGN extends Infernal to make it easier for users to generate large-scale alignments of up to millions of SSU rRNA sequences that will ultimately be used as input to phylogenetic inference methods. (SSU-ALIGN is not capable of inferring phylogenetic trees itself.) Large SSU rRNA sequence datasets are commonly generated by environmental sequencing survey studies that use SSU rRNA as a phylogenetic marker of species in the environment being studied. While designed primarily for these SSU-based studies, SSU-ALIGN is a general tool that can be used to generate alignments of any type of structural RNA, including large subunit ribosomal RNA (LSU rRNA).

The latest release of SSU-ALIGN is 0.1.1 [23 Feb 2016].

The 0.1.1 release is a very minor update to version 0.1 which was the current release for nearly six years. See the v0.1.1 release notes for more information.




Note on SSU-ALIGN and Infernal 1.1

The latest release of SSU-ALIGN (version 0.1.1) includes a version of Infernal much like version 1.0.2. It does not include or use the latest version of Infernal (version 1.1), which is significantly faster than 1.0.2 for RNA homology search. In terms of alignment speed, however, Infernal versions 1.1 and 1.0.2 are comparable, so updating to SSU-ALIGN to use Infernal 1.1 would not have a dramatic effect of running time. Our plan is to eventually update SSU-ALIGN to use Infernal 1.1, but the exact timeframe for that update is currently unclear.

Further reference:

Last modified: Tue Feb 23 16:05:10 2016
Eddy/Rivas Laboratory