Huelsenbeck J, Rannala B: Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context. Science 1997, 276: 227–232.
Article
CAS
PubMed
Google Scholar
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King D, Baertsch R, Blankenberg D, Pond SK, Nekrutenko A, Giardine B, Harris R, Tyekucheva S, Diekhans M, Pringle T, Murphy W, Lesk A, Weinstock G, Lindblad-Toh K, Gibbs R, Lander E, Siepel A, Haussler D, Kent W: 28-way vertebrate alignment and conservation track in the UCSC genome browser. Genome Res. 2007, 17: 1797–1808.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen J, Cooper D, Chuzhanova N, Ferec C, Patrinos G: Gene conversion: mechanisms, evolution and human disease. Nature Reviews Genetics 2007, 8: 762–775.
Article
CAS
PubMed
Google Scholar
Hein J: A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. J. Mol. Evol. 1993, 36: 396–405.
Article
CAS
Google Scholar
Grassly N, Holmes E: A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol. 1997, 14: 239–247.
Article
CAS
PubMed
Google Scholar
Holmes E, Worobey M, Rambaut A: Phylogenetic Evidence for Recombination in Dengue Virus. Mol. Biol. Evol. 1999, 16: 405–409.
Article
CAS
PubMed
Google Scholar
Archibald J, Roger A: Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals. J. Mol. Evol. 2002, 55: 232–245.
Article
CAS
PubMed
Google Scholar
Pond S, Posada D, Gravenor M, Woelk C, Frost S: Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Mol. Biol. Evol. 2006, 23: 1891–1901.
Article
CAS
Google Scholar
Gibbs M, Armstrong J, Gibbs A: Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 2000, 16: 573–582.
Article
CAS
PubMed
Google Scholar
Suchard M, Weiss R, Dorman K, Sinsheimer J: Inferring spatial phylogenetic variation along nucleotie sequences: A multiple changepoint model. J. Am. Stat. Assoc. 2003, 98: 427–437.
Article
Google Scholar
Minin V, Dorman K, Fang F, Suchard M: Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics 2005, 21: 3034–3042.
Article
CAS
PubMed
Google Scholar
Husmeier D: Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics 2005, 21: ii166-ii172.
CAS
PubMed
Google Scholar
Westesson O, Holmes I: Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments. PLoS Comput. Biol. 2009, 5: e1000318.
Article
PubMed Central
PubMed
Google Scholar
Sawyer S: Statistical tests for detecting gene conversion. Mol. Biol. Evol. 1989, 6: 526–538.
CAS
PubMed
Google Scholar
Smith J: Analyzing the mosaic structure of genes. Mol. Biol. Evol. 1992, 16: 1369–1390.
Google Scholar
Siepel A, Korber B: Statistical tests for detecting gene conversion. Mol. Biol. Evol. 1995, 6: 526–538.
Google Scholar
Lole K, Bollinger R, Paranjape R, Gadkari D, Kulkarni S, Novak N, Ingersoll R, Sheppard H, Ray S: Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-InfecteSeroconverters in India, with Evidence of Intersubtype Recombination. J Virol 1999, 73: 152–160.
PubMed Central
CAS
PubMed
Google Scholar
Posada D, Crandall K: Evaluation of methods for detecting recombination from DNA sequences Computer simulations. PNAS 98: 13757–13762.
Martin D, Posada D, Crandall K, Williamson C: A Modified Bootscan Algorithm for Automated Identification of Recombinant Sequences and Recombination Breakpoints. AIDS Res. Hum. Retroviruses 2005, 21: 98–102.
Article
CAS
PubMed
Google Scholar
Boni M, Posada D, Feldman M: An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets. Genetics 2007, 176: 1035–1047.
Article
PubMed Central
CAS
PubMed
Google Scholar
Archer J, Pinney J, Fan J, Simon-Loriere E, Arts E, Negroni M, Robertson D: Identifying the Important HIV-1 Recombination Breakpoints. PLoS. Comput. Biol. 2008, 4: e1000178.
Article
PubMed Central
PubMed
Google Scholar
Hsu C, Zhang Y, Hardison R, Miller W: Whole-Genome Analysis of Gene Conversion Events. In Proceedings of RECOMB Comparative Genomics 2009. Edited by: Ciccarelli F, Miklos I. Budapest, Hungary; 2009:181–192.
Google Scholar
Martin D, Williamson C, Posada D: RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 2005, 21: 260–262.
Article
CAS
PubMed
Google Scholar
Posada D: Evaluation of Methods for Detecting Recombination from DNA sequences: Empirical Data. Mol. Biol. Evol. 19: 708–717.
Mansai S, Innan H: The Power of the Methods for Detecting Interlocus Gene Conversion. Genetics 184: 517–527.
Excoffier L, Novembre J, Schneider S: SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J. Hered. 2000, 91: 506–509.
Article
CAS
PubMed
Google Scholar
Hudson R: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18: 337–338.
Article
CAS
PubMed
Google Scholar
Posada D, Wiuf C: Simulating haplotype blocks in the human genome. Bioinformatics 2003, 19: 289–290.
Article
CAS
PubMed
Google Scholar
Spencer C, Coop G: SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 2004, 20: 3673–3675.
Article
CAS
PubMed
Google Scholar
Mailund T, Schierup M, Pedersen C, Mechlenborg P, Madsen J, Schauser L: CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005, 6: 252.
Article
PubMed Central
PubMed
Google Scholar
Schaffner S, Foo C, Gabriel S, Reich D, Daly M, Altshuler D: Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 2005, 15: 1576–1583.
Article
PubMed Central
CAS
PubMed
Google Scholar
Marjoram P, Wall J: Fast ”coalescent” simulation. BMC Genet. 2006, 7: 16.
Article
PubMed Central
PubMed
Google Scholar
Arenas M, Posada D: Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 2007, 8: 458.
Article
PubMed Central
PubMed
Google Scholar
Hellenthal G, Stephens M: msHOT: modifying Hudson’s ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 2007, 23: 520–521.
Article
CAS
PubMed
Google Scholar
Liang L, Zollner S, Abecasis G: GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 2007, 23: 1565–1567.
Article
CAS
PubMed
Google Scholar
Arenas M, Posada D: Coalescent Simulation of Intracodon Recombination. Genetics 2010, 184: 429–437.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stoye J, Evers D, Meyer F: ROSE: generating sequence families. Bioinformatics 1998, 14: 157–163.
Article
CAS
PubMed
Google Scholar
Rosenberg M: MySSP: non-stationary evolutionary sequence simulation, including indels. Evol. Bioinform. Online 2005, 1: 81–83.
PubMed Central
CAS
Google Scholar
Cartwright R: DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 2005, 21: iii31–38.
Article
CAS
PubMed
Google Scholar
Strope C, Abel K, Scott S, Moriyama E: Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0. Mol. Biol. Evol. 2009, 26: 2581–2593.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kim J, Sinha S: Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics 2010, 11: 54.
Article
PubMed Central
PubMed
Google Scholar
Harris R: Improved pairwise alignment of genomic DNA. PhD thesis. Pennsylvania State University; 2007.
Google Scholar
Hasegawa M, Kishimo M, Yano T: Dating the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985, 22: 160–174.
Article
CAS
PubMed
Google Scholar
Zhang Y, Song G, Vinar T, Green E, Siepel A, Miller W: Reconstructing the evolutionary history of complex human gene clusters. In Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2008). Edited by: Vingron M, Wong L. Singapore; 2008:29–49.
Google Scholar
Siepel A, Bejerano G, Pedersen J, Hinrichs A, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier L, Richards S, Weinstock G, Wilson R, Gibbs R, Kent W, Miller W, D H: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2006, 15: 167–172.
Google Scholar