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Table 2 Definitions of events in the second scenario design (in the DAG)

From: Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios

i

Termini of the edge projected from <e, d>

Triplets

0

Edge is not projected (induction ends)

None

1

<e,х> (х is a leaf cohered with e; induction ends)

<tro,e,d>, <tri,e,х>, <loss,e,d>

2

same as #1

<gain,e,х>

3

<e,d1>

None

4

<e1,d1>; <e2,d2>

None

5

<e2,d1>; <e1,d2>

None

6

<e,d1>

<loss,e,d2>

7

<e,d2>

<loss,e,d1>

8

<e,d1>

None

9

<e,d2>

None

10

<e,d1>

None

11

<e,d2>

None

12

<e1,d>; <e2,d>

<dupl,e,d>

13

<e1,d>; <e2,d>

None

14

<e1,d>; <e2,d>

None

15

<e1,d'>; <e2,d>

<tr+o,e1,d>, <tr+i,e1,d'>

16

<e2,d'>; <e1,d>

<tr+o,e2,d>, <tr+i,e2,d'>

17

<e1,d'>; <e2,d>

<gain,e1,d'>

18

<e2,d'>; <e1,d>

<gain,e2,d'>

19

<e,d*>

<sleep,e,d>

20

<e0,d'>

<gain_big,e,d'>

21

<e,d'1>

<tro,e,d>, <tri,e,d'>, <loss,e,d>

22

<e,d'1>

<gain,e,d'>

23

<e1,d'1>; <e2,d'2>

<tro,e,d>, <tri,e,d'>, <loss,e,d>

24

<e1,d'2>; <e2,d'1>

<tro,e,d>, <tri,e,d'>, <loss,e,d>

25

<e1,d'1>; <e2,d'2>

<gain,e,d'>

26

<e1,d'2>; <e2,d'1>

<gain,e,d'>

27

<e,d'1>

<tro,e,d>, <tri,e,d'>, <loss,e,d>, <loss,e,d'2>

28

<e,d'2>

<tro,e,d>, <tri,e,d'>, <loss,e,d>, <loss,e,d'1>

29

<e,d'1>

<gain,e,d'>, <loss,e,d'2>

30

<e,d'2>

<gain,e,d'>, <loss,e,d'1>

31

<e1,d'>; <e2,d'>

<tro,e,d>, <tri,e,d'>, <loss,e,d>, <dupl,e,d'>

32

<e1,d'>; <e2,d'>

<gain,e,d'>, <dupl,e,d'>

33

<e1,d'>; <e2,d">

<tro,e,d>, <loss,e,d>, <tri,e,d'&d">, <tr+o,e1&e2,d'&d">, <tr+i,e1&e2,d'&d">

34

<e1,d'>; <e2,d">

<gain,e, d'&d">, <tr+o,e1&e2,d'&d">, <tr+i,e1&e2,d'&d">

  1. Consider i the ordering of events specified in Table 1; the second column specifies the termini of the edge projected from the pair <e, d>. The third column specifies triplets to be associated with edges of R j . A notation e1&e2 designates a multiplier of 0.5. In rows 1, 21, 23, 24, 27, 28, 31, 33 the triplets <loss,e,d> designate the loss of the donor copy of the gene after transfer.