Computational protocol: A case for re inventory of Australia’s plant pathogens

Similar protocols

Protocol publication

[…] Selected sequences from five plant pathogenic fungal genera were downloaded from GenBank and aligned using either Clustal X or the online MAFFT server (http://mafft.cbrc.jp/alignment/server/index.html). The alignments were optimised manually to allow maximum alignment and maximum sequence similarity. Gaps were treated as missing data or fifth character states (Mycosphaerella and Phomopsis alignments). Phylogenetic analyses were carried out based on the aligned dataset using PAUP v4.0b10 (). Ambiguously aligned regions were excluded from all analyses, where present. Trees were inferred using the heuristic search option with TBR branch swapping and 100–1 000 random sequence additions. Maxtrees were unlimited, branches of zero length were collapsed, and all multiple parsimonious trees were saved. Trees were drawn in TreeView (). […]

Pipeline specifications

Software tools Clustal W, MAFFT, PAUP*, TreeViewX
Application Phylogenetics