Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores - PubMed (original) (raw)

FIG. 1.

Statistical strategy. In this schematic diagram, ORF 1 finds RBMs in species 1, 2, and S; ORF 2 finds RBMs in species 1, 3, and S; and ORF L finds RBMs in species 2 and S. Thus, _w_1 = {_u_1,1, _u_2,1, . . .}; _w_2 = {u_1,2, . . ., u_L,2}; _w_3 = {_u_2,3, . . .}; and wS = {_u_1,S, _u_2,S, . . ., uL,S}. In this example, ORF 1's set of w values is {_w_1, _w_2, . . ., wS}; ORF 2's set of w values is {_w_1, _w_3, . . ., wS}; and ORF L's set of w values is {_w_2, . . ., wS}. An ORF's set of u values is correlated with its set of w values as described in the text.