Software used in this study.

“Software” provides the name of each computer program or suite of computer programs; “Purpose” describes why this software was used here; “Main web site (URL) or code location” gives the primary Web site for this software; “Bioconda source (if used)” gives the bioconda web site for programs that were installed as bioconda environments; “Online documentation” gives the web site for detailed online manuals, if a given program has one. Publications and arguments for each program are cited and described in Methods. (XLSX)