Characterization of phylogenetic networks with NetTest

BMC Bioinformatics

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).

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