Consensus sequences generated from duiker orthopoxvirus sequencing efforts and alignment file

Sequence file with the consensus orthopoxvirus genomes generated from duikers that were called applying a threshold of 3 unique reads and a majority consensus rule: duiker_pox_updated_consensus, which now includes additional sequencing data for our mapping. To estimate the phylogenetic placement of these three consensus sequences, we first assembled a dataset comprising complete genomes from all but three orthopoxvirus species (the basal Orthopoxvirus raccoonpox, O. skunkpox and O. volepox) and all publicly available genomes assigned by publishing authors to O. cowpox (cowpox viruses are polyphyletic and represent most of the variation within the genus). We aligned the 65 sequences (including our three partial genomes) using MAFFT v7.526 and identified conserved sequence blocks using Gblocks as implemented in SeaView v5. The resulting alignment of 130,439 positions was reduced to 58 unique sequences: orthopoxvirus_duikers_final_scs_mafft_gb_uniq.fst