Computational protocol: Endosymbiotic Bacteria Associated with the Mealy Bug, Rhizoecus amorphophalli (Hemiptera: Pseudococcidae)

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Protocol publication

[…] The nucleotide sequence obtained was processed to remove low quality reads and transformed into consensus sequences with Geneious Pro software version 5.6. The resulted high quality sequences were analyzed with BLASTn (NCBI; http://www.ncbi.nlm.nih.gov) to confirm the authenticity of the isolate. The sequences of related species and genus were downloaded from the Genbank database and a phylogenetic study was carried out with the program MEGA version 5 []. The sequences were aligned using the computer package ClustalW [] and were analyzed to determine the relationships between isolates by the neighbor-joining method [] using the Maximum Composite Likelihood model. Bootstrap values were generated using 2000 replicates to infer the robustness of the tree topology. […]

Pipeline specifications

Software tools Geneious, BLASTN, MEGA, Clustal W
Application Phylogenetics
Organisms Bacillus subtilis, Staphylococcus saprophyticus
Diseases Staphylococcal Infections, Tick Infestations