Table 1.

Numbers and Ratio of Events Reported on Different HGT Penalties

HGT penaltya
Loss eventsb
HGT eventsb
Families in HGTc
16S rRNA tree
    1 9,342 10,468 5,274
    2 14,847 7,374 4,286
    3 21,304 4,702 3,263
    4 26,307 3,191 2,504
    5 29,365 2,474 2,071
Gene content tree
    1 7,055 10,864 5,282
    2 12,413 7,670 4,426
    3 17,557 5,556 3,640
    4 24,004 3,633 2,743
    5 28,144 2,638 2,203
Shuffled tree
    1 10,176 35,942 12,364
    2 17,065 31,664 12,121
    3 29,590 25,966 11,844
    4 50,955 19,104 10,653
    5
62,408
15,842
10,079

a HGT penalty corresponds to the threshold value used

b Loss and HGT events correspond to the number of events observed in the three trees

c Families in HGT corresponds to the number of families predicted to be involved in HGT