2.4. Genome analysis, alignment, and phylogeny
The complete genome sequence of LSDV-WB/IND/19 was aligned with
available genome sequences of other LSDVs from different countries as
well as GTPV and SPPV sequences retrieved from GenBank included in Table
1 using MAFFT (Katoh et al., 2019). A phylogenetic tree was made with
RaxML using the Maximum Likelihood construction method based on the GTR
G+I with 100 bootstrap iterations (Stamatakis, 2014) and visualized by
iTOL (Letunic and Bork, 2021). The nucleotide identities between CaPV
genomes were calculated using the MegAlign program of DNASTAR as per the
Tamura-Nei method (Tamura and Nei, 1993). The pairwise comparison
between LSDV genomes was calculated using the Diffseq program
(https://www.bioinformatics.nl/cgi-bin/emboss/diffseq) whereas
Base‐by‐Base was used to visualize and depict the indels/SNPs (Tu et
al., 2018). Prediction of protein domains was done by InterPro (Blum et
al., 2020).