16S rRNA gene based alignment

2020-01-22T01:07:28Z (GMT) by Laetitia Wilkins David Coil
The 16S rRNA gene sequence from the genome assembly was extracted from RAST by searching for ‘ssu rRNA’ in the function search of the SEED genome browser. Following the protocol outlined in Dunitz et al. (2015), the sequence was uploaded to the Ribosomal Database Project (RDP) and grouped with all sequences in the Pasteurellaceae family and one chosen outgroup, Agarivoran spp., to root the tree. The taxon names from the RDP output file were manually cleaned up and used to build a phylogenetic tree with the program FastTree.