4SIS: Four-sequence Informative Sites Analysis

Description

Two types of informative sites were distinguished, corresponding to the clustering of the putative recombinant with either of the parental representatives. The optimal breakpoint was located by maximizing a chi-square value. Statistical significance was assessed by performing a certain times of permutations and for each permutation, maximizing the chi-sqaure value. The P value reflects the proportion of permutated informative sites, with chi-square values being equal to or greater than the observed value.
Paste your alignment:
4SIS page with example sequences
Or upload the sequence file:
Numbers of simulation:
P value:

Notes:
  1. The program only accepts DNA sequences in fasta format
  2. The order of the taxas in the file MUST be parental representative A, parental representative B, outgroup sequence, putatvie recombinant
  3. The name of the sequences must NOT contain '-'
  4. only deal with the gap-exclusive alignemnt


References:
  • van Cuyck H, Fan J, Robertson DL, Roques P (2005) Evidence of recombination between divergent hepatitis E viruses. Journal of virology, 79(14), 9306-14.
  • Maynard Smith J, Smith NH (1998) Detecting recombination from gene trees. Mol Biol Evol, 15(5), 590-9.
  • Robertson DL, Sharp PM, McCutchan FE, Hahn BH (1995) Recombination in HIV-1. Nature, 374(6518), 124-6.


    • Disclaimer:
    This is not the final release version. If get any problem or suggestion, please contact Jun Fan