Figure 6.

A simple example of the RIO procedure Four bootstrap resampled gene trees are shown. Letters represent sequence names/"functions". "A" (nematode and wheat) are true orthologs of the human query sequence, whereas "B" (rat) is a true paralog of the query (i.e. the first tree happens to be the real one). In 3 out of 4 trees nematode "A" appears orthologous to the query, in 3 out of 4 trees wheat "A" appears orthologous to the query. Rat "B" never appears to be orthologous. For an example of actual RIO output see Figure 7.