3SEQ Recombination Detection Algorithm

This is the official home page for the 3SEQ recombination detection algorithm.   C++ source code, p-value tables, and a manual for the latest version are available from the tabs on the left.

3SEQ is a command-line program that reads in a nucleotide sequence file, in phylip or aligned fasta format, and tests all sequence triplets in the file for a mosaic recombination signal indicating that one of the three sequences (the child) is a recombinant of the other two (the parents).   The statistical test used is a non-parametric test for mosaicism whose p-values should be pre-computed once with the 3SEQ executable (or downloaded).

For bug reports or questions, please feel free to email Maciej Boni at [email protected] or Ha Minh Lam at [email protected]

You can contribute to the repository here.