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As alignment-based methods may be computationally expensive and not scalable to huge datasets, alignment-free methods have been extensively investigated recently.

All sequence datasets, alignments, spreadsheets, annotation files, output files and lists of gene ontology terms for analysis are available at the Dryad link associated with this study.

Figure 1 Core structure and dataset alignment.

As a control, 20 'random sites' were selected by generating random numbers to define the 5' position of sites 20 nucleotides long in the genome dataset alignment; sites that contained gaps were discarded.

The conserved core regions of the coat protein gene sequences were extracted from the genome dataset alignment and used to calculate a neighbor-joining tree using the program MEGA3 [20]; the core regions were those bounded by the sequences encoding the WCIEN and QMKAAA motifs.

The combined dataset alignment consisted of a fragment of 1,526 base pairs (Table  1).

Similarly to GenomeZipper dataset, alignment of reads from BAC pools to Ae. tauschii sequence dataset resulted in a variable number of positive pools per sequence.

The percentage of dots falling in the central area of the triangles was 6.3%, the likelihood map also showed the presence of 93.7% resolved quartets showing that the dataset alignment contained sufficient phylogenetic information.

Performances on PacBio dataset alignments executed with Bowtie2, BWA-MEM, and BLASR are also discussed.

ML analysis on the combined nucleotide dataset alignments was performed in RAxML 7.2.7 [ 74, 75] available on the CIPRES web portal [ 76] with the GTRGAMMA substitution model.

For both datasets, proper alignment is applied to the images based on standard face landmarks.