recipe sina

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: SINA, 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.

package sina

versions:

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, 

1.7.2-0,  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

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:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag>

(see `sina/tags`_ for valid values for ``<tag>``)

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