VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).
:: MORE INFORMATION
Before you download software you need to read disclaimer.