Additional file 1: of General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation

Supplementary methods (sections SM-1 through SM-9), Tables S1 through S4, and Figures S1 through S11. The sections of Supplementary methods describe methodological details on the (analytical and algorithmic) computations of local alignment probabilities (SM-1,2,3,4,5,9) and on the simulation analyses for validating the algorithm (SM-6,7,8). Tables S1-S4 show the results of some analyses. Figures S1, S2, S3 and S11 illustrate some important concepts. Figures S4 and S10 show the results of some analyses. Figures S5, S6, S7 and S8 explain the algorithm implemented in LOLIPOG. Figure S9 shows the phylogenetic trees used for the simulations. (PDF 12355Â kb