Sentence examples for between sequences were calculated from inspiring English sources
Percentage identity and biochemical similarity between sequences were calculated using ProtParam http://www.expasy.ch/tools/protparam.html[ 29].
Pairwise distances between sequences were calculated using TREE-PUZZLE [ 57] using the WAG [ 55] +Γ+I model.
Distances between sequences were calculated by using MEGA version 4 (26 ) with the P-distance analysis option.
Distances between sequences were calculated using the JTT matrix, with and without rate variation among sites (the gamma parameter was set to 1.2).
Distances between sequences were calculated using the FastTree program (Price et al. 2010) that produces log-corrected distances calculated with the BLOSUM45 amino acid similarity matrix.
For each dataset (AAT, OPT, and NRT1/PTR) mean pairwise distances between sequences were calculated and clustered with the neighbor-joining algorithm in PAUP* [ 78].
The percentage of nucleotide identity between sequences was calculated using DnaSP (Librado and Rozas 2009).
P-distance between sequences was calculated for BuT2 and for the nuclear genes using Mega5.2 (Tamura et al. 2011).
Within each Helitron family, the frequency distribution of the number of pair-wise differences between sequences was calculated with Arlequin v. 3.11.
The percentage identity between sequences is calculated with the sequences after the arrow indicated in the figure (the N-terminal end of the molecules which is extremely variable in all vertebrates is not taken into account).
The distance and similarity between sequences are calculated using DNADIST in PHYLIP (package version 3.5c) [ 36] and phylogenetic inference is analyzed using the Neighbor-joining (NJ) method with the Kimura two-parameters substitution model.
