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The final sequence was annotated (File S1) and aligned with reads from massively parallel sequencing of P. taeda genomic DNA, GSS and ESTs (Figure 1; Table 1).

Splice variants were removed from the fully annotated file in order to reduce redundancy of GO IDs.

Since a recognizable protein domain was a requirement, the majority of gene models are functionally annotated (File S3).

Two input formats are accepted for analysis: i) plain DNA sequences in FastA format, ii) a fully annotated file in the Genbank file format.

The tandem sequences were then mapped to the genbank annotated file and the regions overlapping adhesins were compared between all four W. ceti genomes.

To create the input lists of mutations for MutSig, we annotated the muTect and VarScan2 somatic variants with the VEP annotator and we then converted the VCF annotated files in mac format by using the vcf2maf tool (https://github.com/ckandoth/vcf2maf).

Finally, the BioR toolkit supports two command-line utilities for annotating variants: (i) bior_snpeff, which integrates SnpEff annotations (Cingolani et al., 2012), and (ii) bior_vep to annotate files using Ensemble's variant effect predictor (www.ensembl.org/info/docs/variation/vep/).org/info/docs/variation/vep/

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