Figure 1.
(A) The ‘PAML’ tab from IMPACT_S showing the results of the LRT test (M7 vs. M8), (B) Automatically extracted and tabulated ‘BEB results’ table, (C) Mapping of the positively selected sites onto the 3D protein-structure of CRiSPs (2GIZ-A), (D) Tabulated results of ω estimation under the site-specific models (M0, M1, M3, M7 and M8) and (E) The ‘lnL’ table, showing all the log-likelihood values for these models.
Figure 2.
Datamonkey tab and related results.
(A) ‘Datamonkey’ tab showing all the selected options, (B) ‘Common Sites’ table generated from the positive-selection analyses under various methods (SLAC, FEL, REL, MEME and FUBAR) – The sites 110, 172, 202 and 231 (highlighted in pink), were simultaneously detected by Datamonkey, PAML (Codeml) and TreeSAAP as positively-selected (Table S1) [1], (C) ‘Results & 3D’ tab showing the mapping of sites found in the ‘Common Sites’ table.
Figure 3.
Evolutionary Pathway (Evpthwy) tab under TreeSAAP tab and related results.
(A) ‘TreeSAAP’ tab showing the ‘Evpthwy’ tab with results of the CRiSP case study, (B) Gnuplot graph for the property “Average number of surrounding residues” with Z-scores in y-axis and Codon positions in x-axis, (C) ‘PBR’ table showing all ranges (‘From’ - ‘To’) retrieved from the sliding window analysis with the ‘Total’ count of properties for each range and their names [Properties (7–8) (+) (−) – names of properties under significant positive (Z-score ≥3.09) and negative (Z-score ≤3.09) selection, found in the categories 7 and 8].
Figure 4.
Substitutions (Substs) tab under TreeSAAP tab and related results.
(A) ‘TreeSAAP’ tab showing the ‘Substs’ tab and the results of the CRiSPs case study, (B) ‘PBS’ table showing all the significant codons (‘Codon’ column) and the total count (‘Total’ column) of properties for each codon and their respective names [‘Properties (7–8) (+)’ – names of properties under significant (Z-score ≥3.09) positive selection], (C) ‘PBS statistics’, with respect to the PBS table, showing the number of times (‘Total’ column) that the same property (‘Information’ column) is selected across the data set provided and (D) Alignment Filter option with the final view of the alignment containing only the codons from the PBS table with their original positions.
Figure 5.
3D mapping and related functionalities under Results & 3D tab.
(A) ‘Results & 3D’ tab with the results of the CRiSPs case study, (B) ‘MR table’ (Table S3) presenting six columns: ‘Codon’ containing the site found as positive selected (TreeSAAP – Z-score ≥3.09); ‘Datamonkey’ with the positive selected common sites positions from SLAC, FEL, REL, MEME and FUBAR; ‘PAML M8Site’ with the information from BEB results M8; ‘Common Sites’ – reporting the site position common to all the previous mentioned columns; ‘Total’ - count of the number of properties per site; ‘Properties (7–8) (+)’ with the names of properties found under categories 7 and 8 for Z-score ≥3.09, (only common sites are shown and highlighted) (C) 3D structure and ‘PDB Sequence’, mapping the sites positions from the ‘Common Sites’ column following the (D) Merged Results ‘Color Scheme’ according to a pre-defined number of properties: red – less than 2 (NP<2), green - between 2 and 5 (NP(2–5)) and blue - more than 5 (NP>5).