Computational protocol: Sinulariapolydactyla (Ehrenberg, 1834) (Cnidaria, Octocorallia) re-examined, with the description of a new species

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Protocol publication

[…] Published methods () were used to obtain new mtMutS and COI sequences for specimens ZMTAU Co 36607 and Co 36585, collected in 2014 from Eilat, Israel (Gulf of Aqaba, Red Sea), and material from Guam used by (GenBank accession numbers KU230366-KU230389). All other sequences were obtained from GenBank, and have been included in previous phylogenetic analyses (, , ; ) (Suppl. material ). Sequences were aligned using the L-INS-i method in MAFFT (), and evolution models were selected for each gene separately using jModeltest (, ). Maximum likelihood analyses were run using Garli 2.0 () for mtMutS alone and in a combined analysis of mtMutS plus COI with different models of evolution applied to each data partition (mtMutS: HKY+G; COI: HKY+I). Bayesian analyses of the separate (mtMutS) and combined (mtMutS + COI) data sets were run using MrBayes v. 3.2.1 () with the same evolution models applied to separate data partitions. Bayesian analyses were run for 2 million generations (until standard deviation of split partitions < 0.01) with a burn-in of 25% and default Metropolis coupling parameters. MEGA v.5 () was used to calculate pairwise measures of genetic distance (Kimura 2-parameter) among sequences. […]

Pipeline specifications

Software tools MAFFT, jModelTest, GARLI, MrBayes, MEGA-V
Applications Phylogenetics, GWAS