:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'sina' .. highlight: bash sina ==== .. conda:recipe:: sina :replaces_section_title: :noindex: Reference based multiple sequence alignment :homepage: https://github.com/epruesse/SINA :documentation: https://sina.readthedocs.io :license: `GPL / GPLv3 `_ :recipe: /`sina `_/`meta.yaml `_ :links: biotools: :biotools:`SINA`, doi: :doi:`10.1093/bioinformatics/bts252` SINA allows incorporating additional sequences into an existing multiple sequence alignment \(MSA\) without modifying the original alignment. While adding sequences to an MSA with SINA is usually faster than re\-computing the entire MSA from an augmented set of unaligned sequences\, the primary benefit lies in protecting investments made into the original MSA such as manual curation of the alignment\, compute intensive phylogenetic tree reconstruction and taxonomic annotation of the resulting phylogeny. Additionally\, SINA includes a homology search which uses the previously computed alignment to determine the most similar sequences. Based on the search results\, a LCA based classification of the query sequence can be computed using taxonomic classifications assigned to the sequences comprising the reference MSA. SINA is used to compute the small and large subunit ribosomal RNA alignments provided by the SILVA\_ project and is able to use the ARB\_ format reference databases released by the project. .. conda:package:: sina |downloads_sina| |docker_sina| :versions: .. raw:: html
1.7.2-01.7.1-01.7.0-01.6.1-01.6.0-01.5.0-01.4.0-01.3.5-21.3.4-2 ``1.7.2-0``,  ``1.7.1-0``,  ``1.7.0-0``,  ``1.6.1-0``,  ``1.6.0-0``,  ``1.5.0-0``,  ``1.4.0-0``,  ``1.3.5-2``,  ``1.3.4-2``,  ``1.3.1-2``,  ``1.3.1-0``,  ``1.3.0-0`` .. raw:: html
:depends arb-bio-tools: :depends boost-cpp: ``>=1.70.0,<1.70.1.0a0`` :depends glib: ``>=2.58.3,<3.0a0`` :depends libarbdb: ``6.0.6 haa8b8d8_8`` :depends libgcc-ng: ``>=7.5.0`` :depends libstdcxx-ng: ``>=7.5.0`` :depends tbb: ``>=2020.2,<2021.0.0a0`` :depends zlib: ``>=1.2.11,<1.3.0a0`` :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install sina and update with:: mamba update sina To create a new environment, run:: mamba create --name myenvname sina with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/sina: (see `sina/tags`_ for valid values for ````) .. |downloads_sina| image:: https://img.shields.io/conda/dn/bioconda/sina.svg?style=flat :target: https://anaconda.org/bioconda/sina :alt: (downloads) .. |docker_sina| image:: https://quay.io/repository/biocontainers/sina/status :target: https://quay.io/repository/biocontainers/sina .. _`sina/tags`: https://quay.io/repository/biocontainers/sina?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sina/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/sina/README.html