Computational protocol: 16S rDNA based analysis reveals cosmopolitan occurrence but limited diversity of two cyanobacterial lineages with contrasted patterns of intracellular carbonate mineralization

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Protocol publication

[…] Environmental 16S rRNA gene sequences retrieved from our samples were compared with sequences in the GenBank database (http://www.ncbi.nlm.nih.gov/) by BLAST (Altschul et al., ). We retrieved the closest sequences found in the database and included them in an alignment containing also sequences from the closest cultivated members and some representative sequences of major cyanobacterial taxa. Sequences were aligned using MUSCLE (Edgar, ). Ambiguously aligned positions and gaps were eliminated using Gblocks (Castresana, ). The resulting sequence alignments were used as input to build phylogenetic trees by approximate maximum likelihood using Fasttree (Price et al., ) with a General Time Reversible (GTR) model of sequence evolution, and taking among-site rate variation into account by using a four-category discrete approximation of a Γ distribution. ML bootstrap proportions were inferred using 1000 replicates. Trees were visualized with FigTree (http://tree.bio.ed.ac.uk/software/figtree/). […]

Pipeline specifications

Software tools MUSCLE, Gblocks, FastTree, FigTree
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Hemisus marmoratus, Dipturus trachyderma
Chemicals Calcium, Carbonates