Computational protocol: Global Analysis of Arabidopsis/Downy Mildew Interactions Reveals Prevalence of Incomplete Resistance and Rapid Evolution of Pathogen Recognition

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Protocol publication

[…] The 205K small nucleotide polymorphism (SNP) data, published by Atwell et al. , was obtained from the Arabidopsis thaliana polymorphism database (https://cynin.gmi.oeaw.ac.at/home/resources/atpolydb). The SNP data was available for 72 of the 83 accessions used in this study, thus limiting our phylogenetic analysis to those 72 accessions. The phylogenetic relationship was constructed using the Phylip 3.66 software . Specifically, bootstrapping was performed using seqboot with 100 replicates, the distance matrices were built using the dnadist algorithm with default parameters, the trees were made using the Neighbor-Joining algorithm, and the consensus tree was derived with the consense program. The tree was visualized using the TreeView X program . […]

Pipeline specifications

Software tools PHYLIP, TreeViewX
Application Phylogenetics
Organisms Arabidopsis thaliana