Computational protocol: Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology

Similar protocols

Protocol publication

[…] The phylogenetic relationship between species was studied using a combined data set containing ITS, BenA, CaM and RPB2 sequences, individual single gene phylogenies were also generated to resolve relationships among the species. Sequence alignments were generated with MAFFT v. 7 (). The most suitable substitution model was determined using FindModel (). Bayesian analyses were performed with MrBayes v. 3.1.2 (). The sample frequency was set to 100 and the first 25 % of the trees removed as burn-in. Maximum likelihood analyses including 500 bootstrap replicates were run using RAxML (Gamma model of rate heterogeneity) (). Aspergillus flavipes (NRRL 302T) was used as outgroup in the Aspergillus subgenus Nidulantes phylogeny and Aspergillus ustus (CBS 261.67T) as outgroup in the section Nidulantes phylogeny. The resulting trees were visualized with FigTree v1.4.2 and annotated using Adobe Illustrator CS5. BI posterior probabilities (pp) values and bootstrap (bs) percentages of analysis are labelled at the nodes. Values less than 0.95 pp and less than 70 % bs are not shown. Branches with values more than 1 pp and 95 % bs are thickened. Newly obtained sequences were deposited in GenBank. […]

Pipeline specifications

Software tools MAFFT, MrBayes, RAxML, FigTree, Adobe Illustrator
Applications Miscellaneous, Phylogenetics
Chemicals Aflatoxins, Sterigmatocystin, Aflatoxin B1, Echinocandins