The sequences were downloaded from Genbank and aligned using the CLUSTALW alignment of the amino acid sequences.
For phylogenetic analyses, rrs sequences of each of these 15 species were assembled and aligned using the multiple alignment program - ClustalX version 2.0.12 [ 73].
Subsequently, the sequences were imported into the ARB software programme (Ludwig et al. 2004) and aligned using the automatic aligner function.
Subsequently, the sequences were imported into the ARB software program (Ludwig et al. 2004) and aligned using the automatic aligner function.
Subsequently, the sequences were imported into the ARB software package (Ludwig et al. 2004) and aligned using the automatic aligner function.
Consensus sequences were compared against the NCBI GenBank database to confirm species identity [ 58] and aligned using the MUSCLE alignment algorithm [ 59].
To be consistent with the workflow of primates, the yeast-coding sequences were extracted and aligned using the PyCogent codon aligner (see below).
In all, 162 particles on plasmid and 2600 on short DNA were windowed, centred and aligned using the reference-free alignment procedure.
Representative whole genomes (nucleotide) of adenoviral species 1 56 were selected from the National Center for Biotechnology Information (NCBI), and aligned using the EMBL-EBI Clustal Omega tool61,62.
The KD sequences of these proteins were extracted and aligned using the MAFFT program (Katoh and Standley 2013).
DNA sequences were assembled and aligned using the Vector NTI 10.3.0 software package (Invitrogen).
