Supplementary materials :

The sequence data are in "data/*.fa"

The Sankoff matrices are in the directory "parameters/". For example the file "241" includes the Sankoff matrix for gap:tv:ts = 2:4:1.

Trees resulting from each analysis are in the directory "report/newick/", in Newick format (*.tre). For example, the file "16s_241.tre" includes the resulting trees for 16S data, for gap:tv:ts = 2:4:1. "tot_*.tre" are the trees for total data analyses.
Consensus trees in pdf format are to be found in the directory "report/graphconsensus/".

The resulting tree for the reduced analysis is provided in red_tot_111.pdf, with branch length proportional to transformations. Scale

The taxa lists files (for the scripts) are "*.taxa" : "red_list.taxa" for the reduced taxa list, "list.taxa" for the complete taxa list. Since we modified our original taxa names for more comprehensive names in the article, we provide an other list associating "working" names with corresponding label in the article. This list the CSV file "association.csv", colum are separated with comma and there is no text separator. CSV file can be open as a spreadsheet or as a text file.

The general poy script used for the analyses is "script.sh".