Fig. 1

Schematics and demonstration of sitePath. A All sequences but one on the upper side are in a monophyletic group with the purple polymorphism, which is also true for the sequences with the green polymorphism; the ancestral nodes of purple and red overlap on tree trunks so only red is retained, which is also the case for the gold and green polymorphisms. B For site \(X\), the initial entropy \({H}_{0}\) is calculated by clading all sequences as \(\left\{{C}_{1}\right\}\); the minimum entropy \({H}_{min}\) is achieved here when the clade set \(\left\{{C}_{1}, {C}_{2}, {C}_{3}, {C}_{4}\right\}\) is found. The tree is colored according to the polymorphism state of site \(X\) before clading and the dominant polymorphism state after clading. C An example of the resulting clades and mutation detection of the ZIKA virus dataset for site 139 of the polyprotein