Computational protocol: DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior

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Protocol publication

[…] To visualize the phylogenetic position of the 100 most abundant OTUs in the diatom phylogeny, a constraint phylogeny was carried out as explained in Rimet et al. []. Briefly, turtles OTU sequences were aligned with all the rbcL sequences in the R-Syst::diatom library using Muscle [] in Seaview []. The best substitution model was then tested in MEGA7 []. A constraint phylogeny was then calculated in raxmlGUI [] using the fast tree search option. The constraint sequences were the turtle OTUs sequences and the shortest sequences of R-Syst::diatom library. A tree was drawn using the online tool iTOL [] (https://itol.embl.de).A second phylogeny was carried out on Nitzschia inconspicua sequences from the R-Syst::diatom library and their neighbor OTU in the raxmlGUI software using the maximum likelihood and the thorough bootstrap option (see former section). A phylogeny was drawn using Mega7 []. […]

Pipeline specifications

Software tools MUSCLE, SeaView, MEGA, raxmlGUI, iTOL
Databases R-Syst
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Chelonia mydas