<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34420?offset=120 https://bioinformaticsonline.com/bookmarks/view/37572/gtdb-tk-a-toolkit-for-assigning-objective-taxonomic-classifications-to-bacterial-and-archaeal-genomes Wed, 22 Aug 2018 03:21:01 -0500 https://bioinformaticsonline.com/bookmarks/view/37572/gtdb-tk-a-toolkit-for-assigning-objective-taxonomic-classifications-to-bacterial-and-archaeal-genomes <![CDATA[GTDB-Tk: A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.]]> GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. It is computationally efficient and designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).

GTDB-Tk is under active development and validation. Please independently confirm the GTDB-Tk predictions by manually inspecting the tree and bringing any discrepencies to our attention. Notifications about GTDB-Tk releases will be available through the ACE Twitter account (https://twitter.com/ace_uq).

Address of the bookmark: https://github.com/Ecogenomics/GTDBTk

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/39884/retrieving-taxonomic-information-with-r Thu, 29 Aug 2019 01:38:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39884/retrieving-taxonomic-information-with-r <![CDATA[Retrieving Taxonomic Information with R]]> This vignette will introduce users to the retrieval of taxonomic information with myTAI. The taxonomy() function implemented in myTAI relies on the powerful package taxize. Nevertheless, taxonomic information retrieval has been customized for the myTAI standard and for organism specific information retrieval.

Specifically, the taxonomy() function implemented in myTAI can be used to classify genomes according to phylogenetic classification into Phylostrata (Phylostratigraphy) or to retrieve species specific taxonomic information when performing Divergence Stratigraphy (see Introduction for details).

Address of the bookmark: https://cran.r-project.org/web/packages/myTAI/vignettes/Taxonomy.html

]]> Rahul Nayak