Computational protocol: Phylogenetic studies reveal existence of multiple lineages of a single genotype of DENV-1 (genotype III) in India during 1956–2007

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Protocol publication

[…] The CprM gene sequences of fourteen Indian DENV-1 obtained in the present study were submitted to GenBank at (accession numbers are mentioned in Table ). BLAST search was carried-out to confirm the identity of strains. For comparison, we retrieved 11 DENV-1 CprM sequences from India and 70 belonging to diverse geographical locations from the global data base as shown in phylogenetic tree (Figure ). Lasergene 5 software package (DNASTAR Inc, USA) was used to examine the percent identity and diversity among sequences. Sequences were translated into amino acid and aligned using BioEdit v7.0.9. Phylogenetic analysis was carried out using MEGA version 3.1 []. Phylogenetic tree was constructed employing Neighbor Joining method [] with bootstrap analysis of 10000 replicates. […]

Pipeline specifications

Software tools BioEdit, MEGA
Application Phylogenetics
Organisms Dengue virus 1
Diseases Ataxia Telangiectasia