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An example of tracking true orthologs during simulation of duplications. (A) The bold line shows a long orthologous alignment a between two species immediately after they split from their ancestral sequence. (B) A duplication copying A to B in species1 splits a into two alignments a1 and a2, and generates an additional orthologous alignment b. (C) A subsequent duplication copies C to D in species2, splitting a2 and generating c and d, for a total of six orthologous alignment segments.
