How does Bellerophon work?
Bellerophon detects chimeras based on a partial treeing approach (see Ref. 1 below), that is, phylogenetic trees are inferred from independent regions (fragments) of a sequence alignment and the topologies are compared. Incongruencies in branching patterns may be indicative of a chimeric sequence. No trees are actually required to be built during the procedure and the only calculations are distance (similarity) calculations of sequences (see below for a discussion of distance calculations). A full matrix of distances (dm) between all pairs of sequences are calculated for fragments left and right of an assumed conversion point. The total absolute deviation of the distance matrices (distance matrix error dme) of n sequences is then where dm[i][j] denotes the distance between two sequences i and j. To find the sequence with the highest contribution to the dme value, we calculate the ratio of the dme value from all sequences in the dataset over the dme value (dme[i]) when the sequence i th
