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Table 1 Summary of tests applied to the final set of HGT candidates

From: Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer

HGT candidate Number of homologous sequences useda BLAST identity threshold BLAST coverage cut-off Topology changes with different number of sequencesb Topology changes after editing alignment Best model Topology tests (supporting HGT)c Similarities between ML and BI tree reconstruction (%)
HGT1 44 40 90 No No LG + I + G + F ELW, SH 83
HGT2 42 35 85 Yes No LG + G + F n.a. 92
HGT3 54 41 96 Yes No LG + G ELW 100
HGT4 43 40 90 No No LG + G + F n.a. 93
HGT5 53 54 97 No No LG+G+F n.a. 96
HGT6 46 44 90 Yes No WAG + G + F n.a. 95
HGT7 37 35 85 No No LG + I + G + F ELW, SH 84
HGT8 47 28 92 No No LG + I + G + F ELW, SH 93
HGT9 50 37 90 No No LG + G + F ELW, SH 81
HGT10 39 30 75 No No LG + G + F ELW, SH 97
HGT11 44 30 80 No No LG + G + F ELW, SH 89
  1. aAll sequences used have less than 10% of ambiguous quartets in TREE-PUZZLE.
  2. bTaking into account only the relative position of horizontal transfer group into the donor group. Topology changes of branches that do not affect the HGT candidates are not reported.
  3. cELW = Expected Likelihood Weight, SH = Shimodaira and Hasegawa, n.a = not applicable. The groups with homologous sequence only in bacteria are not suitable for topology tests.