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Figure 2. | Standards in Genomic Sciences

Figure 2.

From: Standard operating procedure for computing pangenome trees

Figure 2.

The left panel shows as an example the number of gene families found in 1, 2,…,14 genomes of the 14 completed genomes of Staphylococcus aureus downloaded from NCBI in July 2009. The right panel illustrates three possible weighting schemes. The green bars give weight 1.0 to all gene families except the ORFans, i.e. those gene families only present in one genome, who get weight 0.0 (discarded). The blue bars give a gradually higher weight to the gene families found in the majority of the genomes, the shell. The red bars illustrate the opposite strategy, emphasizing the cloud. All gene families found in the same number of genomes get the same weights.

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