The paper introduces a method called "sister-scanning" (SiScan) for assessing phylogenetic and compositional signals in gene sequences, particularly in the context of recombination. SiScan is designed to directly measure variations in phylogenetic signals due to recombination, test the significance of these variations, and distinguish misleading signals. The method involves a Monte Carlo randomization process where a fourth sequence, acting as an outlier, is used to root the phylogenetic trees and test for significant signals. The authors demonstrate the effectiveness of SiScan using simulated and real viral sequences, showing that it can accurately identify recombinant sites and regions with no clear signal or misleading signals related to compositional similarities. The method is implemented in a program package, SiScan, which is available for download and can be used to analyze nucleotide sequences under MS-DOS. The paper also discusses the broader applications of SiScan in detecting and analyzing recombinant sequences in various biological contexts.The paper introduces a method called "sister-scanning" (SiScan) for assessing phylogenetic and compositional signals in gene sequences, particularly in the context of recombination. SiScan is designed to directly measure variations in phylogenetic signals due to recombination, test the significance of these variations, and distinguish misleading signals. The method involves a Monte Carlo randomization process where a fourth sequence, acting as an outlier, is used to root the phylogenetic trees and test for significant signals. The authors demonstrate the effectiveness of SiScan using simulated and real viral sequences, showing that it can accurately identify recombinant sites and regions with no clear signal or misleading signals related to compositional similarities. The method is implemented in a program package, SiScan, which is available for download and can be used to analyze nucleotide sequences under MS-DOS. The paper also discusses the broader applications of SiScan in detecting and analyzing recombinant sequences in various biological contexts.