Sister-Scanning is a Monte Carlo method for assessing phylogenetic and compositional signals in recombinant sequences. The method, called 'sister-scanning', uses a window to analyze patterns of nucleotide identity between four sequences and calculates Z-scores to test the significance of these signals. It distinguishes between true phylogenetic signals and misleading ones caused by compositional similarities. The method was tested on tobamovirus and luteovirus sequences, where it identified contradictory phylogenetic signals and regions with no clear signal. In the tobamovirus dataset, it detected an interspecies recombination site in the viral RNA-dependent RNA polymerase gene and an unusual pattern of conservation in the three codon positions. The method also includes an option to generate a randomized outlier sequence to test the effects of compositional similarities. The program SiScan is available for download and can be used under MS-DOS. The method was compared with bootstrap analysis and showed that it can detect signals that bootstrap methods may miss. It was also applied to simulated sequences and found to be effective in detecting recombination events. The method was used to analyze luteovirus and tobamovirus sequences, where it identified recombination sites and provided evidence for multiple recombination events. The results suggest that SiScan can be used to detect misleading signals caused by compositional similarities and may have broader applications in phylogenetic analysis.Sister-Scanning is a Monte Carlo method for assessing phylogenetic and compositional signals in recombinant sequences. The method, called 'sister-scanning', uses a window to analyze patterns of nucleotide identity between four sequences and calculates Z-scores to test the significance of these signals. It distinguishes between true phylogenetic signals and misleading ones caused by compositional similarities. The method was tested on tobamovirus and luteovirus sequences, where it identified contradictory phylogenetic signals and regions with no clear signal. In the tobamovirus dataset, it detected an interspecies recombination site in the viral RNA-dependent RNA polymerase gene and an unusual pattern of conservation in the three codon positions. The method also includes an option to generate a randomized outlier sequence to test the effects of compositional similarities. The program SiScan is available for download and can be used under MS-DOS. The method was compared with bootstrap analysis and showed that it can detect signals that bootstrap methods may miss. It was also applied to simulated sequences and found to be effective in detecting recombination events. The method was used to analyze luteovirus and tobamovirus sequences, where it identified recombination sites and provided evidence for multiple recombination events. The results suggest that SiScan can be used to detect misleading signals caused by compositional similarities and may have broader applications in phylogenetic analysis.