References

BARCE

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.

Bootscanning package

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.

CODOUBLE

Detecting and characterizing gene conversion between multigene family members. Drouin G, Prat F, Ell M and Clarke GDP (1999) MOLECULAR BIOLOGY AND EVOLUTION 16:1369-1390.

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

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.

DualBrothers

Dual multiple change-point model leads to more accurate recombination detection. Minin VN, Dorman KS, Fang F and Suchard MA (2005) BIOINFORMATICS 21:3034-3042.

GENECONV (Sawyer's Runs Tests)

Statistical Tests for Detecting Gene Conversion. Sawyer S (1989) MOLECULAR BIOLOGY AND EVOLUTION 6:526-538.

Homoplasy Test

Detecting recombination from gene trees. Maynard Smith J and Smith NH (1998) MOLECULAR BIOLOGY AND EVOLUTION 15:590-599.

JAMBE

Probabilistic Divergence Measures for Detecting Interspecies Recombination. Husmeier D and Wright F (2001) BIOINFORMATCS 17:S123-S131.

LARD

Phylogenetic evidence for recombination in dengue virus. Holmes EC, Worobey M and Rambaut A (1999) MOLECULAR BIOLOGY AND EVOLUTION 16:405-409.

Maximum Chi-Squared Method

Analyzing the Mosaic Structure of Genes. Maynard Smith J (1992) JOURNAL OF MOLECULAR EVOLUTION 34:126-129.

Partimatrix

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.

PhylPro

Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Weiller GF (1998) MOLECULAR BIOLOGY AND EVOLUTION 15:326-335.

PLATO

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.

PIST

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.

RAT

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.

RECOMBINE

Maximum likelihood estimation of recombination rate from population data. Kuhner MK, Yamato J and Felsenstein J (2000) GENETICS 156:1393-401.

RecPars

A heuristic method to reconstruct the history of sequences subject to recombination. Hein J (1993) JOURNAL OF MOLECULAR EVOLUTION 36:396-406.

REGA HIV-1 subtyping tool

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].

Reticulate

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 & RDP2

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.

RIP

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.

SAWYER

Detecting and characterizing gene conversion between multigene family members. Drouin G, Prat F, Ell M and Clarke GDP (1999) MOLECULAR BIOLOGY AND EVOLUTION 16:1369-1390.

implements: Statistical Tests for Detecting Gene Conversion. Sawyer S (1989) MOLECULAR BIOLOGY AND EVOLUTION 6:526-538.

SimPlot

Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW and Ray SC (1999) JOURNAL OF VIROLOGY 73:152-160.

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.

SiScan

Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Gibbs MJ, Armstrong JS and Gibbs AJ (2000) BIOINFORMATICS 16:573-582.

SITES

A coalescent estimator of the population recombination rate. Hey J and Wakeley J (1997) GENETICS 145:833-846.

SNEATHST (Sherman Test)

The effect of evenly spaced constant sites on the distribution of the random division of a molecular sequence. Sneath PHA (1998) BIOINFORMATICS 14:608-616.

STEPHENS

Detecting and characterizing gene conversion between multigene family members. Drouin G, Prat F, Ell M and Clarke GDP (1999) MOLECULAR BIOLOGY AND EVOLUTION 16:1369-1390.

implements: Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Stephens JC (1985) MOLECULAR BIOLOGY AND EVOLUTION 2:539-556.

SERAD

Detection of recombination in DNA multiple alignments with hidden Markov model. Husmeier D and Wright F (2001) JOURNAL OF COMPUTATIONAL BIOLOGY 8:401-27.

TOPAL

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.

VisRD

A novel exploratory method for visual recombination detection. Strimmer K, Forslund K, Holland B, and Moulton V (2003) GENOME BIOLOGY 4:R33.

Phi test

A simple and robust statistical test for detecting the presence of recombination. Bruen T, Philippe H, and Bryant D (2006) GENETICS 172:2665-2681.

4SIS

Evidence of recombination between divergent hepatitis E viruses. van Cuyck H, Fan J, Robertson DL, Roques P. (2005) JOURNAL OF VIROLOGY 79:9306-9314.

FRAG-DIST

Evidence of recombination between divergent hepatitis E viruses. van Cuyck H, Fan J, Robertson DL, Roques P. (2005) JOURNAL OF VIROLOGY 79:9306-9314.

Stepwise

Stepwise detection of recombination breakpoints in sequence alignments. Graham J, McNeney B, Seillier-Moiseiwitsch F. (2005) BIOINFORMATICS 21:589-595.

JPHMM

A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes. Schultz A.-K. et al. BMC BIOINFORMATICS 7:265.

referring page