SINA - reference based multiple sequence alignment
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SINA is a tool to add sequences to an existing multiple sequence
alignment. It needs about 1 second on a single core to add one 16S
full length sequence (about 100k/h on a 32-core workstation). It was
developed to create the multi-million sequence alignment that is the
core of the SILVA SSU and LSU rRNA databases.


Installation
============

* Use the online version hosted by the SILVA project to align small
  batches of LSU and SSU sequences to their databses.

* The preferred way to install SINA locally is via Bioconda (full
  instructions):

     conda create -n sina sina
     conda activate sina


Documentation
=============

* The SINA manual is hosted at readthedocs.

* Please refer to the publication in Bioinformatics for a
  description of the algorithm.

  If you use SINA in your research, please don't forget to cite us:

  Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner; *SINA: Accurate
  high-throughput multiple sequence alignment of ribosomal RNA genes.*
  Bioinformatics 2012; 28 (14): 1823-1829.
  doi:10.1093/bioinformatics/bts252
