Computational protocol: Polyphasic taxonomy of Aspergillus section Candidi based on molecular, morphological and physiological data

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Protocol publication

[…] The sequence data was optimised using the software package Seqman from DNAStar Inc. Sequence alignments were performed by using CLUSTAL-X () and improved manually. The neighbour-joining (NJ) method was used for the phylogenetic analysis. For NJ analysis, the data were first analysed using the Tamura-Nei parameter distance calculation model with gamma-distributed substitution rates (), which were then used to construct the NJ tree with MEGA v. 3.1 (). To determine the support for each clade, a bootstrap analysis was performed with 1000 replications.For parsimony analysis, the PAUP v. 4.0 software was used (Swofford 2002). Alignment gaps were treated as a fifth character state and all characters were unordered and of equal weight. Maximum parsimony analysis was performed for all data sets using the heuristic search option with 100 random taxa additions and tree bisection and reconstruction (TBR) as the branch-swapping algorithm. Branches of zero length were collapsed and all multiple, equally parsimonious trees were saved. The robustness of the trees obtained was evaluated by 1000 bootstrap replications (). An A. flavus isolate was used as outgroup in these experiments. […]

Pipeline specifications

Software tools Clustal W, MEGA-V, PAUP*
Applications Phylogenetics, GWAS
Organisms Aspergillus flavus, Triticum aestivum, Homo sapiens