Table 1

Characterization of TCS networks.

Nature of data sets

POL

COX1

18S

ITS1

Human


Number of data sets

566

1417

2303

191

516


Number of networks generated by TCS

1535

3889

6041

531

1035


Hybrid nodes

495 0.32

891 0.23

914 0.15

117 0.22

124 0.12


Tree

1326

(86.4%)

[0 0.00]

3428

(88.1%)

[0 0.00]

5505

(91.1%)

[0 0.00]

465

(87.6%)

[0 0.00]

952

(92.0%)

[0 0.00]


Galled-tree

1443

(117)

(94.0%)

[131 1.11]

3738

(310)

(96.1%)

[348 1.12]

5873

(368)

(97.2%)

[410 1.11]

507

(42)

(95.5%)

[53 1.26]

1015

(63)

(98.1%)

[67 1.06]


Tree-child

1495

(52)

(97.4%)

[161 3.10]

3799

(61)

(97.7%)

[169 2.77]

5941

(68)

(98.3%)

[179 2.63]

518

(11)

(97.6%)

[27 2.45]

1022

(7)

(98.7%)

[16 2.29]


Tree-sibling

1523

(28)

(99.2%)

[103 3.68]

3865

(66)

(99.4%)

[241 3.65]

6019

(78)

(99.6%)

[232 2.97]

523

(5)

(98.5%)

[11 2.20]

1033

(11)

(99.8%)

[36 3.27]


Uncharacterizable

12

(0.8%)

[100 8.33]

24

(0.6%)

[133 5.54]

22

(0.4%)

[93 4.23]

8

(1.5%)

[26 3.25]

2

(0.2%)

[5 2.50]


For each gene, the table indicates the total number of data sets studied (both databases), the total number of networks generated by TCS, the total number and mean (per network) of reticulate nodes and the number of networks classified as tree, galled-tree, tree-child, and tree-sibling. In parenthesis we indicate the number of networks in that category that did not belong to the previous category and the percentage of characterized networks. In brackets we indicated the number and mean (per network) of reticulate nodes. The last row indicates the number of uncharacterizable networks (i.e., more complex than tree-sibling).

Arenas et al. BMC Bioinformatics 2010 11:268   doi:10.1186/1471-2105-11-268

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