Detecting recombination in 4-taxa DNA sequence alignments with bayesian hidden markov models and markov chain monte carlo. Husmeier D and McGuire G (2003) MOLECULAR BIOLOGY AND EVOLUTION 20:315-37.
Identification of recombination breakpoints in HIV-1 by bootscanning. Salminen M, Carr JK, Burke DS and McCutchan FE (1995) AIDS RESEARCH AND HUMAN RETROVIRUSES 11:1423-1425.
implements: Detecting gene conversion: primate visual pigment genes. Balding DJ, Nichols RA and Hunt DM (1992) PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON B BIOLOGY 249:275-290.
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Rozas J and Rozas R (1999) BIOINFORMATICS 15:174-175.
implements: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Hudson RR and Kaplan NL (1985) GENETICS 111:147-164.
Statistical Tests for Detecting Gene Conversion. Sawyer S (1989) MOLECULAR BIOLOGY AND EVOLUTION 6:526-538.
Detecting recombination from gene trees. Maynard Smith J and Smith NH (1998) MOLECULAR BIOLOGY AND EVOLUTION 15:590-599.
Probabilistic Divergence Measures for Detecting Interspecies Recombination. Husmeier D and Wright F (2001) BIOINFORMATCS 17:S123-S131.
The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments. Jakobsen IB, Wilson SR and Easteal S (1997) MOLECULAR BIOLOGY AND EVOLUTION 14:474-484.
Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Weiller GF (1998) MOLECULAR BIOLOGY AND EVOLUTION 15:326-335.
A likelihood method for the detection of selection and recombination using nucleotide sequences. Grassly NC and Holmes EC (1997) MOLECULAR BIOLOGY AND EVOLUTION 14:239-247.
A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Worobey M (2001) MOLECULAR BIOLOGY AND EVOLUTION 18:1425-1434.
Recombination analysis Tool (RAT): a program for the high-throughput detection of recombination. Etherington GJ, Dicks J and Roberts IN (2005) BIOINFORMATICS 21:278-281.
Maximum likelihood estimation of recombination rate from population data. Kuhner MK, Yamato J and Felsenstein J (2000) GENETICS 156:1393-401.
A heuristic method to reconstruct the history of sequences subject to recombination. Hein J (1993) JOURNAL OF MOLECULAR EVOLUTION 36:396-406.
An automated genotyping system for analysis of HIV-1 and other microbial sequences. de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA, Boucher CA, Camacho R and Vandamme AM (2005) BIOINFORMATICS [Epub ahead of print].
A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Jakobsen IB and Easteal S (1996) COMPUTER APPLICATIONS IN THE BIOSCIENCES 12:291-295.
implements: Detecting evolutionary incompatibilities from protein sequences. Sneath PHA, Sackin MJ and Ambler RP (1975) SYSTEMATIC ZOOLOGY 24:311-332.
RDP: detection of recombination amongst aligned sequences. Martin D and Rybicki E (2000) BIOINFORMATICS 16:562-563.
RDP2: recombination detection and analysis from sequence alignments. Martin DP, Williamson C and Posada D (2004) BIOINFORMATICS 20:1-3.
A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. Siepel AC, Halpern AL, Macken C and Korber BTM (1995) AIDS RESEARCH and HUMAN RETROVIRUSES 11:1413-1416.
implements: Statistical Tests for Detecting Gene Conversion. Sawyer S (1989) MOLECULAR BIOLOGY AND EVOLUTION 6:526-538.
implements: Identification of recombination breakpoints in HIV-1 by bootscanning. Salminen M, Carr JK, Burke DS and McCutchan FE (1995) AIDS RESEARCH AND HUMAN RETROVIRUSES 11:1423-1425, and diversity/similarity plotting.
implements: Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Stephens JC (1985) MOLECULAR BIOLOGY AND EVOLUTION 2:539-556.
A graphical method for detecting recombination in phylogenetic data sets. McGuire G, Wright F and Prentice MJ (1997) MOLECULAR BIOLOGY AND EVOLUTION 14:1125-1131.
TOPAL: recombination detection in DNA and protein sequences. McGuire G and Wright F (1998) BIOINFORMATICS 14:219-220.
TOPAL 2.0: Improved detection of mosaic sequences within multiple alignments. McGuire G Wright F (2000) BIOINFORMATICS, 16:130-134.