Computational protocol: First report of Setaria tundra in roe deer (Capreolus capreolus) from the Iberian Peninsula inferred from molecular data: epidemiological implications

Similar protocols

Protocol publication

[…] Amplicons were sequenced on both strands, and the complementary reads were used to resolve rare, ambiguous base-calls in Sequencher v.4.9. Additionally, BLAST searches were conducted in GenBank and matches with high genetic affinity were downloaded and included in the alignment, with a cut-off point at 91 % genetic similarity. Higher genetic divergence recovered from other homologous sequences from Setaria spp. were downloaded and included in the alignment. The selected outgroup was Thelazia callipaeda. Sequences were aligned in SeaView v.4.2.11 [] under ClustalW2 [] default settings. The most appropriate substitution model for the Bayesian Inference (BI) analysis was determined by the Bayesian Information Criterion (BIC) in jModeltest v.2 []. MrBayes v.3.2.6 [] was used with default priors and Markov chain settings, and with random starting trees. Each run consisted of four chains of 20,000,000 generations, sampled each 10,000 generations and posterior distributions of parameter estimates were visually inspected in Tracer v1.5 []. A plateau was reached after few generations with 25 % of the trees resulting from the analyses discarded as ‘burn-in’. Phylogenetic relationships among haplotypes were estimated using a Maximum Likelihood (ML) approach, as implemented in the software RAxML v7.0.4 [], using the default settings. The 50 % bootstrap consensus tree was built in PAUP 4 []. All analyses were performed through the CIPRES platform []. […]

Pipeline specifications

Software tools Sequencher, SeaView, Clustal W, jModelTest, MrBayes, RAxML, PAUP*
Application Phylogenetics
Organisms Caenorhabditis elegans, Capreolus capreolus