In the case of LINEs, for which we expected multiple subfamilies to exist, sequence divergence was estimated excluding sites inferred to define element subfamilies (see supplementary methods, Supplementary Material online), similar to (Aleshin and Zhi 2010).
Five additional potential recombination events were supported by —four to six methods (supplementary table S2, Supplementary Material online).
Altogether, there are 28 regions common to the three methods (Supplementary Fig. S2C).
Sequence reads with similarity to the mitochondrial genome were filtered out prior to analyses (see supplementary methods, Supplementary Material online).
Number method showed similar results to the risk-weighted surgical pathological methods (Supplementary Figures S2A B).
We built an undirected graph of pairwise sequence similarities to group miRNA arms into families (supplementary methods, Supplementary Material online).
Intron sequences were examined to identify junction motifs and branch points as in other yeasts (supplementary methods, Supplementary Material online).
Methods related to the rate estimations based on Bayesian MCMC analysis are given in the supplementary methods (supplementary tables S2 and S3, Supplementary Material online).
A description of the experimental methods, supplementary figures and tables.
13021_2016_69_MOESM1_ESM.docx Additional file 1. Detailed materials and methods; supplementary tables and figures.
