Computational protocol: Infectious clones of Tomato leaf curl Palampur virus with a defective DNA B and their pseudo-recombination with Tomato leaf curl New Delhi virus

Similar protocols

Protocol publication

[…] The complete nucleotide sequences of clones were determined by dideoxynucleotide chain-termination sequencing using the PCR-based BIG DYE kit (Perkin-Elmer Cetus) and specific internal primers. Sequencing products were resolved commercially (Macrogen, Korea). Sequence information was stored, assembled and analysed using the Lasergene sequence analysis package (DNAStar Inc., Madison, WI, USA) running on an IBM-compatible PC. Phylogenetic analyses were conducted on matrices of aligned sequences using the neighbour-joining and bootstrap options of Phylip (ver. 3.5c) running on an IBM-compatible personal computer. Sequence alignments were produced using CLUSTAL X []. Phylogenetic dendrograms were viewed, manipulated and printed using Treeview []. […]

Pipeline specifications

Software tools PHYLIP, Clustal W, TreeViewX
Application Phylogenetics
Organisms Cucumis melo, Cauliflower mosaic virus
Diseases Infection, HIV Infections