The resulting phylogenetic tree was inspected visually and the Alloteropsis contig was assigned to one of the gene lineages defined based on complete genomes when unambiguously nested in the clade.
The PASC tool is currently based on complete genomes for non-segmented viruses or on one of the genome segments for segmented viruses (e.g., DNA A of geminiviruses).
With the exception of a few population studies based on complete genomes [36], [37] or coding region segments [38], [39], [40], most of the genotyping studies carried out to date were based on control region sequences [8] and/or mtSNPs at a low to moderate level of hg definition [18], [19], [20], [21], [41], [42].
The estimate based on complete genomes was 2008 and had a smaller 95% HPD (2007 2009).
All dates estimated within genotype D were strongly supported by the results based on complete genomes (Table 4).
However, comparisons based on complete genomes from both the mitochondria and the plastids are not available in these cases to assess the potential evolutionary parallels between the organelle genomes.
In some cases, contigs were not assignable to any gene lineage because they were too short or poorly aligned and were consequently positioned outside the groups of orthologs based on complete genomes.
To understand the global relationship between the three genera of the family Filoviridae, we constructed a maximum likelihood tree based on complete genomes of all 80 marburgvirus genomes, the only available complete cuevavirus genome, and 84 non-redundant ebolavirus genomes (Fig. 2).
Cui, Z. et al. Safety assessment of Staphylococcus phages of the family Myoviridae based on complete genome sequences.
In the most complete phylogenetic study of Rickettsia species performed to date, based on complete genome sequences, R. felis was clearly classified within the SFG [32].
