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Both alignments were manually edited (BioEdit), and ambiguously aligned regions and gaps were excluded from further analyses.
Both alignments have three intermediate stations.
Both alignments were tested for recombination with the Single Breakpoint Recombination SBPP) tool [87] in the DATAMONKEY web-server [88]; evidence for recombination, inferred by the small sample AIC score, was only found for HIV-1 Control dataset.
Both alignments gave the same tree topologies.
Both alignments can be downloaded from our webpage.
Both alignments are available for download (Supplementary data [ 39]).
Both alignments have the same nucleotide composition and the same frequency of nucleotides per column.
Both alignments produced identical and significantly supported branching patterns among genera.
Both alignments are tightly coupled as is the case for covariance models themselves.
Both alignments in the single-stranded (ss) and double-stranded (ds) regions can contribute to the final RSmatch score.
Both alignments (the shuffled and unshuffled) are analyzed in the normal RNAz prediction pipeline as described above.
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