Phylogenetic diversity of metagenome assembled genomes (MAGs) from bank vole (Myodes glareolus) gut microbiota.
datasetposted on 16.09.2020 by Rob Knight, Timothy A Mousseau, Tapio Mappes, Eugene Tukalenko, Phillip Watts, Anton Lavrinienko, Luke Thompson
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Concatenated alignment of 16 ribosomal proteins (L2, L3, L4, L5, L6, L14, L16, L18, L22, L24, S3, S8, S10, S17 and S19) identified in bank vole (Myodes glareolus) gut bacteria (metagenome assembled genomes, MAGs) and bacterial reference genomes obtained from Genbank. Data were obtained by (1) searching for the 16 phylogenetic markers from the MAGs and the reference genomes using HMMSEARCH43 in HMMER v.3.1b2, then (2) aligning data using MUSCLE45 v.3.8.31, (3) trimming the alignments using TRIMAL46 v.1.2rev59, and (4) concatenating the alignments using the CONCAT script implemented by BINSANITY. A detailed protocol for this phylogenomic workflow can be found at ProtocolsIO (dx.doi.org/10.17504/protocols.io.mp5c5q6).