Computational protocol: The First Identified Citrus tristeza virus Isolate of Turkey Contains a Mixture of Mild and Severe Strains

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Protocol publication

[…] The cloned CP and RdRp genes were sequenced in both directions by automated cycle sequencing using M13 forward and reverse primers. The sequences of the CP and RdRp genes were assembled and analyzed using Vector NTI Suite program (Invitrogen, USA). The sequences were compared with each other and other CP and RdRp gene sequences in the GenBank. Multiple sequence alignments of the full-length amino acid sequences of the CP and the RdRp genes were conducted by the AlignX Module of Vector NTI Suite. The phylogenetic analysis was performed by Clustal X2 program using neighbor joining algorithm and tested by a bootstrap analysis with 1000 replications. Constructed phylogenetic trees were visualized by TreeView program. […]

Pipeline specifications

Software tools Vector NTI Advance, Clustal W, TreeViewX
Applications Phylogenetics, Protein sequence analysis
Organisms Citrus tristeza virus, Meleagris gallopavo
Diseases Retinal Telangiectasis, Coinfection