Computational protocol: A new approach to species delimitation in Septoria

Similar protocols

Protocol publication

[…] A basic alignment of the obtained sequence data was first done using MAFFT v. 7 (http://mafft.cbrc.jp/alignment/server/index.html; ) and if necessary, manually improved in BioEdit v. 7.0.5.2 (). To check the congruency of the multigene dataset, a 70 % neighbour-joining (NJ) reciprocal bootstrap method with maximum likelihood distance was performed (, ). Bayesian analyses (critical value for the topological convergence diagnostic set to 0.01) were performed on the concatenated loci using MrBayes v. 3.2.1 () as described by Crous et al. () using nucleotide substitution models that were selected using MrModeltest () (). [...] The inter-and intraspecific distances for each individual dataset were calculated using MEGA v. 4.0 () with the Kimura-2-parameter (pairwise deletion) model. […]

Pipeline specifications

Software tools MAFFT, BioEdit, MrBayes, MrModelTest, MEGA-V
Applications Phylogenetics, GWAS