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Repository sina
Name: sina
Owner: iuc
Synopsis: SINA reference based multiple sequence alignment
SINA aligns nucleotide sequences to match a pre-existing MSA using a graph based alignment algorithm similar to PoA. The graph approach allows SINA to incorporate information from many reference sequences building without blurring highly variable regions. While pure NAST implementations depend highly on finding a good match in the reference database, SINA is able to align sequences relatively distant to references with good quality and will yield a robust result for query sequences with many close reference.
Content homepage: https://sina.readthedocs.io/en/latest/
Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/iuc/sina/8afa8799d50f
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/sina
Type: unrestricted
Revision: 3:8afa8799d50f
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Repository README files - may contain important installation or license information

Readme files
**Add reference libraries** [Reference databases](https://www.arb-silva.de/download/arb-files/) provided by the [SILVA project](https://www.arb-silva.de/) can be used within this wrapper by adding the corresponding files to the tool-data directory and editing `tool-data/sina_references.loc.sample` as follows: `LSU_Parc ${__HERE__}/SILVA_132_LSUParc_12_12_17_opt.arb` `LSU_Ref ${__HERE__}/SILVA_132_LSURef_07_12_17_opt.arb` `SSU_Ref ${__HERE__}/SILVA_132_SSURef_12_12_17_opt.arb` `Ref_NR_99 ${__HERE__}/SILVA_132_SSURef_NR99_13_12_17_opt.arb`

Contents of this repository

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Name Description Version Minimum Galaxy Version
reference based multiple sequence alignment 1.6.1+galaxy0 18.01

Categories
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis