Computational protocol: Lungworm seroprevalence in free-ranging harbour seals and molecular characterisation of marine mammal MSP

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Protocol publication

[…] For phylogenetic analyses, intron sequences were removed from the genomic MSP sequences to compare coding sections only. MSP nucleotide and deduced amino acid sequences of harbour seal and harbour porpoise nematodes were compared to those of nematodes affecting terrestrial animals. The sequences were aligned with the Clustal W method and phylogenetic analyses were performed by bootstrap tests of phylogeny (1000 replicates) using the maximum likelihood method of the software package MEGA 6.0 (), respectively. The best fit model was determined comparing maximum likelihood fits of 24 different nucleotide substitution models including General Time Reversible (GTR), Hasegawa-Kishino-Yano (HKY), Tamura-Nei (TN93), Tamura 3-parameter (T92), Kimura 2-parameter (K2), Jukes-Cantor (JC) and maximum likelihood fits of 48 different amino acid substitution models including General Time Reversible (GTR), Jones-Taylor-Thornton (JTT), General Reverse Transcriptase (rtREV), General Reversible Chloroplast (cpREV), General Reversible Mitochondrial (mtREV24). Models were determined in consideration of the corrected Akaike Information Criterion (AICc), the Bayesian Information Criterion (BIC), the Maximum Likelihood value (InL) and the number of parameters (including branch lengths) by using the software MEGA 6.0 (, ). […]

Pipeline specifications

Software tools Clustal W, MEGA
Application Phylogenetics
Organisms Phoca vitulina, Homo sapiens, Dictyocaulus viviparus, Bos taurus, Caenorhabditis elegans
Diseases Bronchopneumonia, Infection