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SINA | High-throughput multiple sequence alignment of ribosomal RNA genes

Aligns and optionally taxonomically classifies ribosomal RNA (rRNA gene sequences). SINA is part of the rRNA gene processing pipeline of the SILVA ribosomal databases project. The software can execute a homology search based on the computed alignment and generate a per sequence classifications from the search results. It also allows to convert reference alignments from FASTA to ARB format. SINA was compared with the commonly used high throughput multiple sequence alignment (MSA) programs PyNAST and mothur.

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SINA classification

SINA specifications

Unique identifier:
Command line interface, Web user interface
Input data:
An rRNA gene sequence.
Operating system:
SILVA Incremental Aligner
Restrictions to use:
Academic or non-commercial use
Input format:
Computer skills:

SINA support



  • Elmar Pruesse <>


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Max Planck Institute for Marine Microbiology, Microbial Genomics Group, Bremen, Germany; Jacobs University Bremen, School of Engineering and Sciences, Bremen, Germany; Ribocon GmbH, Bremen, Germany

Funding source(s)

This research was funded by the Max Planck Society (MPS).

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