Computational protocol: DNA barcoding of morphologically characterized mosquitoes belonging to the subfamily Culicinae from Sri Lanka

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Protocol publication

[…] The trace files/chromatograms of cox1 and ITS2 sequences were manually edited using BioEdit software. Sequences of low quality were excluded during data analysis. Consensus sequences were aligned using Clustal W in BioEdit software. Once the alignment was completed, species identification was confirmed by comparison to publicly available sequence data in GenBank using Basic Logical Alignment Search Tool (BLAST) [] and the Barcode of Life Database (BOLD) interface [www.boldsystems. org]. The number of parsimony informative sites, number of variable sites, number of haplotypes, haplotype diversity and GC content were analyzed using the DNA Sequences Polymorphism software (DnaSP, version 5.1.10). MEGA version 6.0 was used to calculate intraspecific and interspecific pairwise sequence divergence using the Kimura-2 parameter distance model []. Neighbor-Joining (NJ) phylogenetic trees of cox1 and ITS2 sequences were constructed in MEGA 6.0 using Kumura-2 Parameter distances. Branch support of NJ trees were assessed by bootstrapping with 1000 replicates. Codon positions included 1st + 2nd + 3rd + noncoding regions. All the haplotype sequences of cox1 and ITS2 were deposited in the GenBank database (see below). […]

Pipeline specifications

Software tools BioEdit, Clustal W, DnaSP, MEGA
Application Phylogenetics
Organisms Aedes aegypti, Homo sapiens