Computational protocol: The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops

Similar protocols

Protocol publication

[…] Sequence alignments for 44 isolates were made for the two loci (ITS and cox1) using ClustalW in Bio-Edit and manually edited afterwards. Of these 44 isolates, 30 isolates represented the clade 8b strains that were sequenced in this study; the other 14 isolates represent species of the other clade 8 subclades (8a, 8c and 8d) and their sequences were derived from Q-bank (www.q-bank.eu) or from GenBank (www.ncbi.nlm.nih.gov). For each locus, two different phylogenetic analyses were performed, one using Maximum Likelihood analysis as implemented in the MEGA5 software () and the other using Bayesian Inference of Phylogeny (MrBayes v. 3.1.2; , ). Model selection was done by jModeltest (, ) with the Akaike Information Criterion (AIC). The model that best fitted the data and that was available in MEGA5 and MrBayes was the General Time Reversible model with gamma distributed rate variation (GTR + G). For the Maximum Likelihood phylogenetic analysis, the data were described as coding (cox1) or non-coding (ITS). A bootstrap consensus tree inferred from 1 000 replicates was built. For the Bayesian analysis, two analyses were run simultaneously for 1 000 000 generations with three heated chains and one cold chain. The majority-rule consensus tree was calculated after discarding the first 250 000 generations (25 %) from each run as burn-in.Both alignments, trees, as well as the phylogenetic source files are available on TreeBASE (study number 13805). […]

Pipeline specifications

Software tools Clustal W, MEGA, MrBayes, jModelTest
Application Phylogenetics