Figure 1

Overview of AIR-package. Overview of the functionalities and programs in the AIR-package installed on the Bioportal: The colored boxes depict input files (red), output files (green), and the AIR programs (Blue). Texts in Italics depict the filename and respective extension of output files of AIR programs. A) AIR-Appender uses several single gene alignments for construction of a multigene alignment. B) AIR-Identifier uses the output file from AIR-Appender and file containing one or more phylogenetic trees for calculating site rates and rate categories. C. AIR-Remover deletes fast evolving sites according to settings defined by the user. The output files from each of the AIR programs can be used in subsequent analysis by copying the files from the work directory to project folder on the Bioportal using the copy home function. Five main output files are produced by AIR. In which two are graphical html files with information about site rates and fast evolving sites (rates.html), and sites removed from the alignment (outfile.html). File 'rates.html' shows the rate categories as different colors (up to 8 categories), while 'outfile.html' shows the removed sites in red color (e.g. category 7 and 8 removed are shown in red), and rest sites in blue. Files namely 'rates' and 'out.ctl' are produced by PAML programs, which are implemented in AIR-Identifier. While 'outfile.ali' is the multigene alignment with fast evolving sites removed.