Patterns of gappy alignments. Rows represent individual sequences, and black regions indicate missing data. A. A concatenated alignment of three genes, not all of which have been obtained from all species. B. Gap patterns used for the artificial alignments. Each gap pattern is based on a single gene family in the Phytome database. The total percentage of missing amino acids for each alignment is as follows. 1: 14%; 2: 21%; 3: 20%; 4: 29%; 5: 46%; 6: 54%; 7: 55%; 8: 60%; 9: 56%; 10: 58%. C. Example of column-deleted and random-deleted control alignments. The examples shown contain the same percentage of missing amino acids as gap pattern 4 in panel B.