Computational protocol: DNA Barcodes for the FIshes of the Narmada, One of India’s Longest Rivers

Similar protocols

Protocol publication

[…] Sequence alignment and assembly was carried out using Codon code Aligner v.3.0.1 (CodonCode Corporation) and MEGA 5 . Sequence divergence values within and among species were employed the Kimura two parameter (K2P) model using analytical functions on BOLD v3.1 (www.boldsystems.org). A neighbor joining (NJ) tree based on K2P distance, nearest neighbor analysis (NN), and nucleotide composition values were also obtained using BOLD. The analysis of genetic distances was complemented by downloading of related sequences from GenBank for comparison with specimens of Labeo dyocheilus, Puntius sarana, Liza subviridis, Nematalosa japonica and Mystus spp. These species have deep divergence values that can lead to puzzling identifications. In these and other cases, we have used the ABGD (automated barcode gap discovery) interface web tool available at: http://wwwabi.snv.jussieu.fr/public/abgd/abgdweb.html . For the analysis the ABGD method was first implemented using default parameters and Kimura 2-parameter (K2P) distances to correct for transition rate bias (relative to transversions) in the substitutions . The default for the minimum relative gap width was set to different values between 0 and 1.2. Sequences were aligned and submitted to BOLD project code DBFN and Genbank with accession numbers JX983210–JX983514 () (dx.doi.org/10.5883/DS-NFDB). […]

Pipeline specifications

Software tools MEGA, ABGD
Application Population genetic analysis