SINA stand-alone binaries

Download Links

 

SINA v1.2.11:
Centos 5.8: Initiates file download64-bit
Ubuntu 12.04: Initiates file download64-bit Initiates file download32-bit
Ubuntu 10.04: Initiates file download64-bit Initiates file download32-bit
Manual: Initiates file downloadPDF

The binaries compiled for Centos 5.8 should work on most Linux distributions. If you are having trouble, please contact us at Opens window for sending emailcontact(at)arb-silva.de.

Older Versions are accessible via the Opens internal link in current windowarchive.

 

By downloading SINA you agree to the SINA Personal Use and Evaluation License (see below).

Documentation

 
Citing SINA:

SINA: accurate high throughput multiple sequence alignment of ribosomal RNA genes
Elmar Pruesse; Jörg Peplies; Frank Oliver Glöckner
Bioinformatics 2012; doi: Opens external link in new window10.1093/bioinformatics/bts252


Manual:

A short manual explaining the command line usage of SINA can be found here:

SINA user manual (PDF).

The manual is also packaged with the SINA binaries in "man" format.


License:

The SINA stand-alone binaries are available under a Personal Use and Evaluation License.

For your convenience, SINA is packaged together with the required components from the ARB software package. These files are subject to the ARB copyright and license. We have permission to distribute these components with SINA, but please do not redistribute them. Instead, get the official ARB version directly from their home page.


Getting started:

  1. Unpack the archive
    $ tar -xvzf sina-1.2.10.tgz
  2. Change into the unpacked directory and check that SINA is working
    $ cd sina-1.2.10
    $ ./sina --version
    SINA v1.2.10 (svn-20432)
  3. Get yourself a suitable reference alignment. For SSU and LSU, the Opens internal link in current windowSILVA NR datasets are a good starting point. Alternatively, if you have some other reference alignment you want to use in multi-FASTA format, convert it to ARB format like this:
    $ ./sina -i reference.fasta -o reference.arb --prealigned
    Make sure it's valid multi-FASTA though. The first word of each header must be unique for each sequence!
  4. Try aligning some sequences:
    $ ./sina -i mysequences.fasta -o aligned.fasta --ptdb reference.arb
    The first time you do that, the ARB PT server used by SINA to quickly find reference sequences for alignment will build it's index. This may take a while, but you will only have to repeat this if you change the reference alignment. The PT server will also continue to run. Use  "killall arb_pt_server" to stop all your running PT servers.
  5. If you used the SILVA NR dataset, you can classify your sequences like this:
    $ ./sina -i mysequences.fasta -o aligned.arb --ptdb reference.arb \
    --search --search-db reference.arb \
    --lca-fields tax_slv
  6. Check the manual to find out about the rest of the options.
    $ ./sina manual
  7. Have fun, find out something great and cite us when you publish! :)


Contact:

If you experience problems with running SINA, send us a mail at Opens window for sending emailmailto:contact@arb-silva.de.

Personal Use and Evaluation License (PUEL) for SINA Stand-Alone Software

 

This license applies if you download the SINA Stand-Alone Software Package (the "Product") from www.arb-silva.de. In summary, the license allows you to use the Product free of charge for academic Personal Use or, alternatively, for non-academic, time-limited Evaluation.

 

Overview:

Personal Use (academic) is when you install the Product yourself and you make use of it. You can use the Product within an academic study to process as much data as you like and publish the processed data as long as you follow the terms below. If you deploy the Product to a single or multiple computers for colleagues within your institution, e.g. in the capacity as a system administrator, this would no longer qualify as Personal Use.

Personal Use does NOT include (1) any redistribution of the Product, (2) any kind of Product-based data analysis service for third parties, or (3) integration of the Product into another software.

 

License Agreement:

License version 1, September 7, 2011

RIBOCON GMBH (“OWNER”) IS WILLING TO LICENSE THE PRODUCT (AS DE‐
FINED IN § 1 BELOW) TO YOU ONLY UPON THE CONDITION THAT YOU AC‐
CEPT ALL OF THE TERMS CONTAINED IN THIS PERSONAL USE AND EVALUA‐
TION LICENSE AGREEMENT FOR THE SINA STAND‐ALONE SOFTWARE (“AGREE‐
MENT”). PLEASE READ THE AGREEMENT CAREFULLY. BY DOWNLOADING OR
INSTALLING THE PRODUCT, YOU ACCEPT THE FULL TERMS OF THIS AGREE‐
MENT.

§ 1 Subject of Agreement. “Product”, as referred to in this
Agreement, shall be the software package “SINA Stand‐Alone” which
allows for the accurate high throughput multiple sequence align‐
ment of ribosomal RNA genes. The Product consists of executable
files in machine code for Unix‐based operating systems as well as
other data files as required by the executable files at run‐time
and documentation in electronic form. The Product includes all
documentation and updates provided to you by Owner under this
Agreement and the terms of this Agreement will apply to all such
documentation and updates unless a different license is provided
with an update or documentation.

§ 2 Grant of license. Owner grants you a personal, non‐exclu‐
sive, non‐transferable, limited license without fees to repro‐
duce, install, execute, and use internally the Product for your
Personal Use or Evaluation. “Personal Use” applies to academic
use and requires that you use the Product on the same host com‐
puter where you installed it yourself and that no more than one
client connect to that host computer at a time for the purpose of
using the Product remotely. “Evaluation” applies to non‐academic
use and means testing the Product for a period of two weeks; af‐
ter expiry of that term, you are no longer permitted to evaluate
the Product.

§ 3 Restrictions and Reservation of Rights. (1) Any use beyond
the provisions of § 2 is prohibited. The Product and copies
thereof provided to you under this Agreement are licensed, not
sold, to you by Owner and the author of the Product reserves all
copyrights and other intellectual property rights.

(2) You may not do any of the following: (a) provide access, dis‐
tribute or otherwise transfer the Product to any other person;
(b) use the Product for the provision of any kind of service for
the benefit of any other person or of a third party; (c) modify
the Product. However if the documentation accompanying Product
lists specific portions of Product, such as header files, class
libraries, reference source code, and/or redistributable files,
that may be handled differently, you may do so only as provided
in the documentation; (d) decompile, or reverse engineer the
Product; (e) integrate the Product into another software. This
does not apply as far as applicable law may require otherwise or
if Owner grants you additional rights of use in a separate agree‐
ment in writing.

(3) The Product is not designed, licensed or intended for use in
the design, construction, operation or maintenance of mass de‐
struction/biological weapons and Owner and its licensors disclaim
any express or implied warranty of fitness for such uses.

§ 4 Termination. The Agreement is effective on the Date you re‐
ceive the Product and remains effective until terminated. Your
rights under this Agreement will terminate immediately without
notice from Owner if you materially breach it or take any action
in derogation of Owner’s and/or its licensors’ rights to Product.
Owner may terminate this Agreement should any Product become, or
in Owner’s reasonable opinion likely to become, the subject of a
claim of intellectual property infringement or trade secret mis‐
appropriation. Upon termination, you will cease use of, and de‐
stroy, Product and confirm compliance in writing to Owner. Sec‐
tions 3‐8, inclusive, will survive termination of the Agreement.

§ 5 Disclaimer of Warranty. TO THE EXTENT NOT PROHIBITED BY AP‐
PLICABLE LAW, OWNER PROVIDES THE PRODUCT “AS IS” WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIM‐
ITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE OR NON‐INFRINGEMENT, EXCEPT TO THE EXTENT THAT
THESE DISCLAIMERS ARE HELD TO BE LEGALLY INVALID. The entire risk
as to the quality and performance of the Product is with you.
Should it prove defective, you assume the cost of all necessary
servicing, repair, or correction. In addition, Owner shall be al‐
lowed to provide updates to the Product in urgent cases. You are
then obliged to install such updates. Such an urgent case in‐
cludes, but is not limited to, a claim of rights to the Product
by a third party.

§ 6 Limitation of Liability. TO THE EXTENT NOT PROHIBITED BY AP‐
PLICABLE LAW, IN NO EVENT WILL OWNER OR ITS LICENSORS BE LIABLE
FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR SPECIAL, INDIRECT,
CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED RE‐
GARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF OR RELATED TO
THE USE OF OR INABILITY TO USE PRODUCT, EVEN IF OWNER HAS BEEN
ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. In no event will Own‐
er’s liability to you, whether in contract, tort (including neg‐
ligence), or otherwise, exceed the amount paid by you for Product
under this Agreement. Some states do not allow the exclusion of
incidental or consequential damages, so some of the terms above
may not be applicable to you.

§ 7 Third Party Code. Portions of Product may be provided with
notices and open source licenses from communities and third par‐
ties that govern the use of those portions, and any licenses
granted hereunder do not alter any rights and obligations you may
have under such open source licenses, however, the disclaimer of
warranty and limitation of liability provisions in this Agreement
will apply to all the Product.

§ 8 General. Failure by Owner to enforce any particular term of
this Agreement shall not be construed as a waiver of any of its
rights under it. The illegality, invalidity or unenforceability
of any part of this Agreement will not affect the legality, va‐
lidity or enforceability of the remainder. If you and the Owner
have signed a separate written licence agreement covering the use
of the Product, the terms of such signed licence agreement shall
take precedence over any conflicting terms of this Agreement.
Otherwise this Agreement constitutes the entire agreement between
the parties in relation to the Product and its licensing and su‐
persedes any other oral or written communications, agreements or
representations with respect to the Product. The construction,
validity and performance of this Agreement shall be governed by
and submitted to the laws of the Federal Republic of Germany and
the nonexclusive jurisdiction of the courts of the Federal Repub‐
lic of Germany. Notwithstanding the foregoing, Owner and its li‐
censors shall have the right to seek injunctive, or similar, re‐
lief in any courts of competent jurisdiction.

 

The author of SINA reserves all copyrights and other intellectual property rights. All further rights are at Ribocon GmbH (the "Owner") in legal agreement with the author of SINA and all third parties involved.

If you are interested in commercial use of the SILVA stand-alone software contact sina(at)ribocon.com