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ARG construction To construct the ARG, we first inferred the ancestral state of each position in the Progressive Cactus ancestral penguin genome Anc05, which is basal to all penguins, by aligning against positions in the ancestral waterbird genome (Anc05) using a custom tool we developed, halAncestralAlleles ( We then inferred ARGs across the contigs at least 1 Mb in size, and fewer than 25% unspecified ancestral alleles, in the A9 genome, spanning 1.13 Gbp and accounting for 83.24% of the genome length, using tsinfer v.0.4.1 (ref
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